Table S1

Table S1. Btau_4.0 cattle CNV regions and their frequencies in the resource Angus population (472 animals). No

Chr

Start

End

Length

Typea

1 2 3 4 5 6

chr1 chr1 chr1 chr1 chr1 chr1

12,265,746 14,914,756 16,511,615 16,769,382 18,244,759 21,620,367

12,544,191 15,043,994 16,692,314 17,278,945 18,362,369 21,693,775

278,446 129,239 180,700 509,564 117,611 73,409

loss loss loss both gain loss

7 8 9

chr1 chr1 chr1

22,838,393 23,876,732 27,204,282

22,921,098 24,000,231 27,415,115

82,706 123,500 210,834

gain gain loss

10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

27,818,390 29,975,903 31,352,734 32,192,771 32,949,575 39,429,582 40,691,263 41,248,664 44,961,871 45,512,563 49,589,647 51,972,286 53,960,828 57,774,377 59,799,327

28,339,282 30,036,543 31,580,518 32,491,089 34,085,800 39,716,032 40,758,983 41,306,130 45,023,386 46,114,237 49,754,204 52,172,542 54,041,510 57,829,164 59,825,125

520,893 60,641 227,785 298,319 1,136,226 286,451 67,721 57,467 61,516 601,675 164,558 200,257 80,683 54,788 25,799

gain gain loss gain both gain gain loss gain both loss gain gain gain loss

25 26

chr1 chr1

66,797,200 68,100,506

66,903,183 68,188,517

105,984 88,012

both gain

27 28 29

chr1 chr1 chr1

71,699,084 77,503,532 86,023,955

71,812,294 77,735,937 86,164,725

113,211 232,406 140,771

gain loss gain

StartSNPb

EndSNPc

No. SNPd

No.Animale

Frequencyf

BTB-00005637 BTB-00502247 ARS-BFGL-NGS-41853 BTB-01083949 BTB-01511655 Hapmap34985BES1_Contig424_935 BTB-00011076 ARS-BFGL-BAC-16283 Hapmap51561-BTA120459 BTB-00011225 Hapmap40010-BTA-59286 BTB-00013847 ARS-BFGL-NGS-80747 BTB-00014686 BTA-16749-no-rs ARS-BFGL-NGS-55025 BTA-122545-no-rs ARS-BFGL-NGS-106743 ARS-BFGL-NGS-57355 BTB-01645280 BTB-00023604 BTB-01712157 BTA-25403-no-rs ARS-USMARC-ParentDQ404150-rs29012530 ARS-BFGL-BAC-19440 Hapmap29526-BTA124137 ARS-BFGL-NGS-20101 BTA-116098-no-rs ARS-BFGL-NGS-16561

Hapmap60346-rs29019231 ARS-BFGL-BAC-12976 Hapmap51162-BTA-118728 BTB-01083468 BTB-01931918 BTB-01210232

4 4 6 16 4 3

3 2 1 11 1 1

0.64% Multiple Unique 2.33% Unique

BTB-01668820 BTA-49319-no-rs Hapmap33501-BTA-152681

3 4 5

1 1 3

Hapmap26636-BTA-123832 ARS-BFGL-BAC-11193 BTB-01653794 BTB-00014284 BTB-00902144 BTA-07775-no-rs Hapmap38790-BTA-87413 Hapmap51160-BTA-117818 ARS-BFGL-NGS-64154 BTB-02044553 Hapmap50572-BTA-113037 BTA-100076-no-rs ARS-BFGL-NGS-27112 ARS-BFGL-NGS-21622 UA-IFASA-2169

8 3 4 8 28 6 3 3 3 12 6 6 3 3 3

3 1 4 2 33 48 1 1 1 6 4 1 1 1 1

ARS-BFGL-NGS-61672 UA-IFASA-7116

4 3

3 1

ARS-BFGL-NGS-5124 BTA-95638-no-rs Hapmap38311-BTA-39536

3 7 4

1 4 2

Unique Unique Unique 0.64% 0.64% Unique 0.85% Multiple 6.99% 10.17% Unique Unique Unique 1.27% 0.85% Unique Unique Unique Unique 0.64% Unique Unique 0.85% Multiple

30 31 32 33 34 35 36 37 38 39 40 41 42 43

chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1 chr1

90,954,551 94,303,131 94,470,192 95,245,457 95,518,231 104,031,791 104,370,684 121,811,393 123,116,252 123,423,499 124,499,732 129,075,421 130,937,338 134,419,503

91,050,019 94,369,685 94,958,244 95,384,347 95,898,816 104,164,419 104,729,910 122,002,734 123,225,467 123,610,350 124,554,177 129,373,663 131,023,932 134,900,836

95,469 66,555 488,053 138,891 380,586 132,629 359,227 191,342 109,216 186,852 54,446 298,243 86,595 481,334

both loss both gain both gain loss gain loss both gain gain gain both

44

chr1

135,176,080

135,258,763

82,684

gain

45 46 47 48 49 50


146,723,389 150,892,465 372,647 1,402,725 2,724,987 4,373,397

146,829,619 150,948,126 437,813 1,525,206 2,920,608 4,478,568

106,231 55,662 65,167 122,482 195,622 105,172

gain both loss gain gain gain

51 52

chr2 chr2

8,160,688 9,337,707

8,215,583 9,590,181

54,896 252,475

gain loss

53 54 55 56 57 58 59 60 61

chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2 chr2

12,924,309 17,232,240 18,415,238 21,388,968 22,966,997 30,526,227 30,892,143 31,936,465 32,515,385

13,076,787 17,468,224 18,531,691 21,493,899 23,064,597 30,598,831 31,050,611 32,232,984 32,615,890

152,479 235,985 116,454 104,932 97,601 72,605 158,469 296,520 100,506

gain loss gain loss gain loss loss both gain

BTB-01196514 ARS-BFGL-NGS-39699 Hapmap54865-rs29015706 Hapmap42562-BTA-48245 Hapmap42952-BTA-48143 BTB-01810872 BTB-00047301 ARS-BFGL-BAC-13578 BFGL-NGS-114386 Hapmap51836-BTA-49378 BTB-01694723 ARS-BFGL-NGS-9109 Hapmap58543-rs29022778 Hapmap45405-BTA111896 Hapmap24138-BTA124742 ARS-BFGL-NGS-33058 ARS-BFGL-NGS-7667 ARS-BFGL-NGS-11180 Hapmap58923-rs29010138 ARS-BFGL-NGS-6024 Hapmap34854BES4_Contig206_568 BTB-01717869 Hapmap50551-BTA104382 ARS-BFGL-NGS-84317 BTB-00080955 ARS-BFGL-NGS-104601 BFGL-NGS-118009 BTB-00084791 Hapmap61002-rs29016992 ARS-BFGL-NGS-64281 ARS-BFGL-BAC-30866 Hapmap52594-rs29026993

ARS-BFGL-NGS-16663 Hapmap52705-rs29019397 BTA-07846-rs29027508 Hapmap41001-BTA-48148 Hapmap42235-BTA-50604 BTB-00807095 BTB-00046888 BTA-120125-no-rs BFGL-NGS-119141 Hapmap43795-BTA-16918 ARS-BFGL-NGS-39073 Hapmap27857-BTA-124684 BFGL-NGS-116159 BTB-01215148

4 3 9 4 9 4 11 7 4 6 3 9 4 10

2 1 5 1 6 1 3 3 1 9 1 3 1 11

BTA-11882-no-rs

3

1

Hapmap57299-ss46527085 Hapmap22921-BTA-124887 BTB-01204311 BTA-105370-no-rs ARS-BFGL-NGS-103086 ARS-BFGL-NGS-105116

3 3 3 5 3 4

1 2 1 3 1 1

BTA-85707-no-rs Hapmap43273-BTA-47993

3 9

2 6

BTB-01808519 BTA-49759-no-rs Hapmap46225-BTA-49570 BTA-46844-no-rs BTB-00084660 BTB-01817112 Hapmap23355-BTA-133816 BFGL-NGS-112255 BTB-01571963

5 5 4 4 4 3 6 11 4

1 1 2 1 1 1 1 4 2

Multiple Unique 1.06% Unique 1.27% Unique 0.64% 0.64% Unique 1.91% Unique 0.64% Unique 2.33% Unique Unique Multiple Unique 0.64% Unique Unique Multiple 1.27% Unique Unique Multiple Unique Unique Unique Unique 0.85% Multiple

62 63 64 65 66 67 68 69 70 71 72 73 74 75


33,101,143 34,345,939 34,720,067 39,844,697 40,726,084 41,304,216 41,943,024 42,132,665 43,164,686 43,818,479 56,098,625 58,227,705 61,390,455 61,839,493

33,321,372 34,401,741 34,839,746 39,991,756 40,796,451 41,373,884 42,045,139 42,191,064 43,558,749 43,987,549 56,291,807 58,626,068 61,579,008 61,895,925

220,230 55,803 119,680 147,060 70,368 69,669 102,116 58,400 394,064 169,071 193,183 398,364 188,554 56,433

loss gain loss gain gain gain both gain both gain loss both gain gain

76 77 78 79

chr2 chr2 chr2 chr2

62,216,870 62,689,753 70,726,543 72,164,866

62,293,568 62,843,802 70,962,445 72,362,724

76,699 154,050 235,903 197,859

gain both both loss

80 81 82 83

chr2 chr2 chr2 chr2

79,325,692 81,059,213 81,679,349 84,885,301

79,691,370 81,288,597 81,725,075 85,391,095

365,679 229,385 45,727 505,795

loss gain loss both

84 85 86

chr2 chr2 chr2

86,531,280 87,287,499 91,619,250

86,763,945 87,677,142 91,815,686

232,666 389,644 196,437

gain loss gain

87 88 89 90 91 92 93

chr2 chr2 chr2 chr2 chr2 chr2 chr2

101,047,483 107,310,683 111,736,094 114,553,299 118,685,524 123,657,396 127,692,028

101,230,934 107,523,930 111,893,421 114,734,314 118,803,647 123,727,853 127,831,357

183,452 213,248 157,328 181,016 118,124 70,458 139,330

gain gain loss loss gain gain gain

BTB-00093291 BTB-00094203 ARS-BFGL-NGS-7878 ARS-BFGL-NGS-20574 ARS-BFGL-BAC-2813 BFGL-NGS-118508 ARS-BFGL-BAC-41569 BTA-08061-no-rs BTA-47437-no-rs BTB-01242289 BTB-01390827 ARS-BFGL-NGS-105321 ARS-BFGL-NGS-5784 Hapmap31501-BTA158286 ARS-BFGL-NGS-9262 BTB-00100191 BTB-01601989 Hapmap28506-BTA151467 ARS-BFGL-NGS-32409 BTB-00102386 BTB-01549373 Hapmap33253-BTA160512 BTA-48277-no-rs BTA-114138-no-rs Hapmap51556-BTA116563 ARS-BFGL-NGS-33331 ARS-BFGL-NGS-94750 Hapmap50373-BTA-48875 ARS-BFGL-NGS-90923 Hapmap43218-BTA-26258 Hapmap43869-BTA-49512 BTA-49605-no-rs

Hapmap42950-BTA-47265 ARS-BFGL-NGS-6378 BTB-00093713 UA-IFASA-9548 ARS-BFGL-NGS-103291 Hapmap28052-BTA-156755 ARS-BFGL-NGS-92476 Hapmap43158-BTA-113479 BTB-01878940 ARS-BFGL-NGS-4574 Hapmap43801-BTA-18254 BTA-106070-no-rs BTA-23960-no-rs BTA-28581-no-rs

8 3 3 4 3 3 4 3 12 4 7 12 3 3

1 1 1 1 1 1 2 1 6 1 3 16 1 1

Hapmap51412-BTA-16926 ARS-BFGL-NGS-86934 BTB-01297078 BTB-00121035

4 5 6 5

1 2 10 1

ARS-BFGL-NGS-104820 BTA-98942-no-rs Hapmap26185-BTA-157573 BTA-105824-no-rs

8 6 3 5

6 2 1 11

ARS-BFGL-NGS-104699 Hapmap26980-BTA-149220 ARS-BFGL-NGS-94983

6 8 6

2 4 10

Hapmap51953-BTA-48787 ARS-BFGL-NGS-102802 ARS-BFGL-NGS-78963 Hapmap32590-BTA-147852 BTB-01343496 Hapmap40273-BTA-49510 ARS-BFGL-NGS-90958

3 5 6 4 4 3 4

1 2 1 1 1 1 3

Unique Unique Unique Unique Unique Unique Multiple Unique 1.27% Unique 0.64% 3.39% Unique Unique Unique Multiple 2.12% Unique 1.27% Multiple Unique 2.33% Multiple 0.85% 2.12% Unique Multiple Unique Unique Unique Unique 0.64%

94 95 96 97 98

chr2 chr2 chr2 chr2 chr3

131,588,874 137,116,058 139,455,987 140,506,974 4,958,546

131,746,090 137,217,212 139,551,340 140,625,558 5,011,827

157,217 101,155 95,354 118,585 53,282

both loss loss gain gain

99 100 101 102 103 104 105 106 107 108 109 110 111

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3

6,885,989 12,903,718 14,499,634 15,957,682 24,418,803 33,023,094 34,956,496 36,163,190 39,603,165 42,117,153 42,320,544 42,649,870 43,284,601

7,009,487 13,253,595 14,589,463 16,093,450 24,739,952 33,334,174 35,174,031 36,432,761 39,904,291 42,265,299 42,444,472 42,811,618 43,404,040

123,499 349,878 89,830 135,769 321,150 311,081 217,536 269,572 301,127 148,147 123,929 161,749 119,440

loss gain gain gain gain gain loss both loss loss gain both loss

112 113 114 115 116 117 118 119 120 121

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3

44,048,765 46,852,798 49,817,047 50,585,133 51,012,902 57,559,243 57,878,378 63,999,689 68,215,262 71,099,159

44,239,452 47,187,220 49,905,825 50,700,761 51,080,481 57,647,236 58,101,023 64,276,929 68,946,016 71,294,714

190,688 334,423 88,779 115,629 67,580 87,994 222,646 277,241 730,755 195,556

gain gain loss loss gain gain gain gain both loss

122 123 124 125 126


74,265,240 80,265,230 81,419,939 82,102,949 84,953,502

74,512,971 80,591,322 81,487,137 82,133,546 85,101,877

247,732 326,093 67,199 30,598 148,376

loss gain gain both gain

BFGL-NGS-114532 ARS-BFGL-BAC-33280 BFGL-NGS-111732 BTA-49790-no-rs Hapmap44676-BTA111644 BTB-01333281 ARS-BFGL-NGS-25865 BFGL-NGS-110108 ARS-BFGL-NGS-84180 ARS-BFGL-NGS-41773 BFGL-NGS-116953 ARS-BFGL-NGS-5984 ARS-BFGL-NGS-99357 Hapmap43012-BTA-67593 Hapmap60829-rs29020073 ARS-BFGL-NGS-24876 INRA-424 Hapmap43129-BTA105623 BTA-119268-no-rs BFGL-NGS-110746 BTB-01608596 BTB-00462925 BTB-00127988 INRA-240 INRA-405 Hapmap56074-rs29026779 BTA-68164-no-rs Hapmap41426-BTA109878 BTB-00134661 BTB-01850782 BTB-00136493 BTB-01509140 BTB-01155798

ARS-BFGL-NGS-58272 ARS-BFGL-NGS-39399 BTB-01349081 BFGL-NGS-116761 Hapmap29230-BTA-156201

4 4 4 5 3

2 1 1 1 1

BTB-01678060 INRA-237 ARS-BFGL-NGS-3037 Hapmap44611-BTA-66646 Hapmap26676-BTA-141146 BTB-00125265 ARS-BFGL-NGS-85942 ARS-BFGL-NGS-35338 BTA-67567-no-rs BTB-01155098 ARS-BFGL-NGS-96237 BTB-01436085 BTB-01704990

5 4 3 6 11 7 4 7 8 5 4 5 5

1 2 3 2 33 1 1 4 1 1 1 3 1

ARS-BFGL-NGS-38892 ARS-BFGL-NGS-33061 BTB-01898997 Hapmap44321-BTA-96862 BTB-01649999 BTB-00128908 ARS-BFGL-NGS-33752 Hapmap55559-rs29014148 BTA-118180-no-rs BTB-01203844

5 8 4 4 3 4 5 8 21 4

2 1 2 1 1 1 1 2 18 1

Hapmap51849-BTA-68314 ARS-BFGL-NGS-16740 BTB-02080963 BTA-13007-rs29017974 BTB-01155932

8 5 4 3 5

1 2 1 3 2

Multiple Unique Unique Unique Unique Unique Multiple 0.64% Multiple 6.99% Unique Unique 0.85% Unique Unique Unique 0.64% Unique Multiple Unique Multiple Unique Unique Unique Unique Multiple 3.81% Unique Unique Multiple Unique 0.64% Multiple

127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150

chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr3 chr4 chr4 chr4 chr4 chr4

86,479,894 86,929,987 89,088,339 91,831,643 97,854,125 98,122,606 99,943,369 101,563,252 102,006,659 109,933,002 112,092,553 112,885,093 117,579,920 124,993,618 125,459,677 125,868,208 126,213,166 127,158,903 127,404,886 212,683 3,765,511 8,585,313 14,278,865 15,178,812

86,622,155 87,102,164 89,150,703 91,968,396 98,059,928 98,167,287 100,281,682 101,666,585 102,465,179 110,063,000 112,139,188 113,039,037 117,705,066 125,114,116 125,637,877 126,049,084 126,273,096 127,265,328 127,465,651 308,908 3,885,050 8,655,767 14,343,312 15,404,245

142,262 172,178 62,365 136,754 205,804 44,682 338,314 103,334 458,521 129,999 46,636 153,945 125,147 120,499 178,201 180,877 59,931 106,426 60,766 96,226 119,540 70,455 64,448 225,434

gain both both gain gain loss both gain both gain gain loss both loss gain gain gain gain gain gain gain gain loss gain

151

chr4

19,293,733

19,674,049

380,317

loss

152 153 154 155 156 157 158 159

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4

21,992,116 23,540,614 25,546,708 25,686,933 30,647,622 33,429,202 37,122,658 38,486,603

22,039,295 23,703,769 25,639,733 25,743,842 30,801,551 33,581,735 37,278,954 38,777,811

47,180 163,156 93,026 56,910 153,930 152,534 156,297 291,209

gain loss gain gain gain gain loss both

BTB-00138938 Hapmap43912-BTA-68491 BTB-00140409 BTB-01240613 ARS-BFGL-NGS-58887 BFGL-NGS-118592 BTB-01600271 BTB-00145986 BTB-02090559 ARS-BFGL-NGS-107996 Hapmap48972-BTA-98997 BTB-01932810 BTB-00156662 ARS-BFGL-NGS-26624 BTA-94635-no-rs ARS-BFGL-NGS-20403 ARS-BFGL-NGS-92456 ARS-BFGL-NGS-10085 Hapmap52284-rs29018845 ARS-BFGL-NGS-102812 BFGL-NGS-117422 Hapmap60503-rs29018741 Hapmap43542-BTA-27796 Hapmap43169-BTA119396 Hapmap33778-BTA141931 BTA-72397-no-rs BTB-00169017 BTB-01768855 Hapmap43716-BTA-87799 ARS-BFGL-NGS-24570 BTA-69987-no-rs BTB-01812529 Hapmap33483-BTA142021

Hapmap51621-BTA-68487 ARS-BFGL-NGS-31952 BTB-00140470 BTB-01240416 ARS-BFGL-NGS-1062 ARS-BFGL-NGS-40486 BTB-01517782 BTB-00146049 BTB-00147091 ARS-BFGL-NGS-29420 Hapmap52612-rs29022803 ARS-BFGL-NGS-27698 BTB-00156807 ARS-BFGL-NGS-90439 ARS-BFGL-NGS-1743 BTB-00161805 ARS-BFGL-NGS-1034 ARS-BFGL-NGS-76685 ARS-BFGL-NGS-4905 BTA-113672-no-rs Hapmap23596-BTA-149292 BTB-01951988 ARS-BFGL-NGS-89632 BTA-71206-no-rs

5 7 3 4 6 3 9 4 11 5 3 6 5 5 6 6 3 5 3 3 3 3 3 5

1 2 5 1 1 2 2 1 3 1 1 2 2 1 4 1 1 1 1 1 1 1 1 3

BTB-01238546

7

2

BTB-00168676 BTB-01581687 BTA-72712-no-rs BTB-01912042 ARS-BFGL-NGS-14672 Hapmap60347-rs29020617 BTB-01547771 Hapmap60522-rs29015286

3 5 3 3 4 3 6 9

1 1 2 1 1 1 1 2

Unique Multiple 1.06% Unique Unique Multiple Multiple Unique 0.64% Unique Unique Multiple Multiple Unique 0.85% Unique Unique Unique Unique Unique Unique Unique Unique 0.64% Multiple Unique Unique Multiple Unique Unique Unique Unique Multiple

160 161 162 163

chr4 chr4 chr4 chr4

39,744,935 40,597,911 43,321,794 45,884,388

40,280,466 40,957,217 43,532,790 46,072,693

535,532 359,307 210,997 188,306

both both both gain

BTA-70243-no-rs BTA-21017-no-rs BTB-00178816 BTB-00181826

Hapmap24263-BTA-161141 Hapmap53600-rs29010856 BTB-00179180 BTB-01721944

13 10 9 7

6 3 17 1

164 165 166 167

chr4 chr4 chr4 chr4

47,627,222 50,360,660 55,243,287 55,953,228

47,698,509 50,471,395 55,327,035 56,008,311

71,288 110,736 83,749 55,084

gain both loss loss

1 5 1 1


60,120,348 60,378,727 61,278,329 67,668,287 69,715,087 71,540,167 82,824,272

60,181,301 60,455,507 61,386,843 67,786,346 69,828,238 71,668,855 82,894,901

60,954 76,781 108,515 118,060 113,152 128,689 70,630

gain loss gain gain gain both gain

ARS-BFGL-NGS-23878 Hapmap44277-BTA-70372 BTB-01066167 Hapmap35290BES8_Contig586_984 BTA-123277-no-rs ARS-BFGL-NGS-28532 BTB-00190258 Hapmap43717-BTA-87854 BTB-00195350 ARS-BFGL-NGS-7407 BTB-01162037

3 4 3 3

168 169 170 171 172 173 174

3 3 4 3 4 5 3

2 1 1 1 1 2 1

175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192

chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr4 chr5

83,611,096 86,213,244 87,082,107 88,395,912 92,136,302 92,658,825 95,741,416 96,699,110 98,823,259 103,370,909 109,357,491 111,422,402 112,250,879 117,147,050 117,762,273 118,846,747 122,019,575 8,534

83,797,597 86,372,608 87,535,150 88,748,827 92,221,551 92,825,921 95,888,948 96,757,469 98,898,746 103,534,136 109,690,847 111,584,899 112,321,308 117,572,536 117,854,165 118,913,504 122,159,188 74,229

186,502 159,365 453,044 352,916 85,250 167,097 147,533 58,360 75,488 163,228 333,357 162,498 70,430 425,487 91,893 66,758 139,614 65,696

gain gain both loss gain both gain gain gain gain gain gain loss gain gain loss gain gain

ARS-BFGL-NGS-108242 Hapmap28169-BTA-70367 BTB-01066119 Hapmap33484-BTA142221 BTB-01640588 BFGL-NGS-109868 BTB-00189909 BTB-01392065 BTA-71050-no-rs ARS-BFGL-NGS-37048 Hapmap46191-BTA101479 Hapmap40292-BTA-71565 BTB-01857387 BTA-16834-no-rs Hapmap58175-rs29027322 BTB-01323946 ARS-BFGL-NGS-95211 ARS-BFGL-NGS-22270 ARS-BFGL-NGS-98418 BTA-71716-no-rs ARS-BFGL-NGS-15146 ARS-BFGL-NGS-78121 ARS-BFGL-NGS-91867 ARS-BFGL-NGS-27142 ARS-BFGL-NGS-74214 ARS-BFGL-NGS-103689 BTB-00210179 ARS-BFGL-NGS-44782 BTB-01498887

BTA-71571-no-rs BTA-96831-no-rs BTB-01443471 Hapmap39421-BTA-65907 BTA-119205-no-rs BTB-01313094 ARS-BFGL-NGS-104187 BTB-00202516 BTB-00204531 BTA-71832-no-rs BTB-02023900 ARS-BFGL-NGS-14130 BTA-72255-no-rs Hapmap59459-rs29011115 ARS-BFGL-NGS-25593 Hapmap29532-BTA-142672 BFGL-NGS-118785 ARS-BFGL-NGS-26008

5 6 13 11 4 6 3 3 3 5 4 5 3 12 5 3 6 3

2 1 7 1 1 4 1 1 1 1 3 5 1 5 2 1 1 1

1.27% 0.64% 3.60% Unique Unique 1.06% Unique Unique Multiple Unique Unique Unique Unique Multiple Unique Multiple Unique 1.48% Unique Unique 0.85% Unique Unique Unique Unique 0.64% 1.06% Unique 1.06% Multiple Unique Unique Unique

193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212

chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5 chr5

243,281 3,563,151 4,046,316 7,334,735 10,052,609 13,197,167 13,505,734 16,957,758 20,300,856 21,856,103 23,700,171 33,471,333 38,997,928 40,207,559 44,049,852 47,021,993 50,654,895 52,621,362 53,230,936 54,725,318

533,660 3,858,443 4,129,013 7,384,620 10,134,451 13,241,405 13,694,971 17,163,849 20,380,401 21,921,042 23,812,682 33,711,793 39,161,931 40,345,773 44,146,732 47,169,582 50,698,220 52,807,103 53,527,535 54,790,930

290,380 295,293 82,698 49,886 81,843 44,239 189,238 206,092 79,546 64,940 112,512 240,461 164,004 138,215 96,881 147,590 43,326 185,742 296,600 65,613

gain loss loss gain gain loss gain both loss loss gain gain gain gain both loss gain gain gain gain

213 214 215 216 217 218 219 220 221 222 223 224 225 226 227


60,293,217 63,031,140 64,141,257 99,108,572 109,932,423 116,152,846 122,410,166 123,453,977 123,934,422 124,980,157 125,618,716 6,133,489 6,757,367 7,091,617 7,741,467

60,570,822 63,559,392 64,253,582 99,656,228 110,191,418 116,198,060 122,453,525 123,508,157 123,998,440 125,087,083 125,669,489 6,208,393 6,845,580 7,136,902 7,920,291

277,606 528,253 112,326 547,657 258,996 45,215 43,360 54,181 64,019 106,927 50,774 74,905 88,214 45,286 178,825

gain both gain both gain gain loss gain loss both gain gain gain gain loss

BTB-02030231 Hapmap44365-BTA-28169 ARS-BFGL-NGS-27281 ARS-BFGL-NGS-82536 BTB-00235905 Hapmap55297-rs29017245 BTB-00223109 BTA-87039-no-rs Hapmap45956-BTA-74297 DIAS-20 BTA-72805-no-rs ARS-BFGL-NGS-18775 Hapmap42995-BTA-60519 BTB-01248659 BTB-01144774 BTA-73478-no-rs BFGL-NGS-118441 DIAS-90 DIAS-93 Hapmap28821-BTA159936 BFGL-NGS-117229 BTA-87618-no-rs ARS-BFGL-NGS-44413 Hapmap43798-BTA-17697 BTA-94395-no-rs Hapmap52801-ss46526219 Hapmap43673-BTA-75237 BTB-00239093 ARS-BFGL-NGS-80676 BTA-32202-no-rs ARS-BFGL-NGS-21723 BTB-01848340 BTB-01596025 Hapmap51311-BTA-76381 BTB-00242660

BTB-02048207 BTB-00909797 Hapmap48402-BTA-60008 ARS-BFGL-NGS-97510 ARS-BFGL-NGS-27890 Hapmap52005-BTA-75510 Hapmap60169-rs29019788 BTA-87049-no-rs BTA-74304-no-rs DIAS-19 ARS-BFGL-NGS-7668 Hapmap59321-rs29015703 ARS-BFGL-NGS-66566 BTB-01832706 BTB-01494277 DIAS-86 Hapmap58456-rs29022391 BTA-27449-no-rs BTA-27472-no-rs Hapmap29845-BTA-152324

5 10 3 3 3 3 4 7 4 3 3 6 4 4 5 4 3 5 6 3

2 3 2 1 1 1 1 11 3 4 1 2 1 1 2 1 1 1 5 1

Hapmap44616-BTA-73618 Hapmap41489-BTA-24267 BTB-01636697 BFGL-NGS-116999 Hapmap40294-BTA-89295 ARS-BFGL-NGS-104298 ARS-BFGL-NGS-53194 ARS-BFGL-NGS-72362 ARS-BFGL-NGS-6245 BTA-04955-rs29015305 ARS-BFGL-NGS-18125 ARS-BFGL-NGS-26083 Hapmap29564-BTA-143742 ARS-BFGL-NGS-101160 BFGL-NGS-109742

6 9 4 13 7 3 3 3 3 4 3 3 4 3 6

9 89 8 4 37 1 1 1 1 4 3 4 1 1 1

Multiple 0.64% Multiple Unique Unique Unique Unique 2.33% 0.64% 0.85% Unique Multiple Unique Unique Multiple Unique Unique Unique 1.06% Unique 1.91% 18.86% 1.69% 0.85% 7.84% Unique Unique Unique Unique 0.85% 0.64% 0.85% Unique Unique Unique

228 229 230 231 232 233


8,628,612 10,600,743 12,191,817 14,619,692 22,877,833 24,595,803

10,046,379 10,762,144 12,472,476 14,683,309 22,959,300 24,758,573

1,417,768 161,402 280,660 63,618 81,468 162,771

both both loss gain both loss

234 235 236 237 238 239 240


35,250,054 38,212,942 39,052,609 39,915,858 41,276,776 44,273,421 46,560,134

35,462,920 38,326,148 39,223,438 39,997,429 41,323,841 44,433,640 46,639,540

212,867 113,207 170,830 81,572 47,066 160,220 79,407

gain both loss gain loss both gain

BTA-111598-no-rs BTB-01322092 BTB-01685239 BFGL-NGS-117043 BTB-01313885 Hapmap23485-BTA150182 BTA-75768-no-rs Hapmap27083-BTC-041166 Hapmap27344-BTC-063259 Hapmap27326-BTC-051854 Hapmap24437-BTC-037637 Hapmap27102-BTC-054991 ARS-BFGL-NGS-95035

241

chr6

47,058,970

47,210,710

151,741

gain

BTA-76119-no-rs

242 243

chr6 chr6

48,018,897 48,862,294

48,130,754 49,042,264

111,858 179,971

loss loss

244 245 246 247 248


50,691,754 50,980,972 52,438,316 53,483,561 54,415,176

50,860,417 51,063,101 52,708,577 53,719,949 54,503,529

168,664 82,130 270,262 236,389 88,354

loss loss loss gain gain

249 250 251 252 253 254 255 256 257


56,471,463 57,416,735 60,904,765 61,382,450 64,178,161 67,307,791 73,412,899 76,498,800 78,652,911

56,662,125 57,612,503 61,049,599 61,569,919 64,260,179 67,395,438 73,591,857 76,626,037 78,780,301

190,663 195,769 144,835 187,470 82,019 87,648 178,959 127,238 127,391

loss gain gain loss gain gain gain gain both

258

chr6

78,855,305

78,919,443

64,139

gain

Hapmap39432-BTA-76145 ARS-USMARC-ParentAY849380-no-rs BTB-01382552 Hapmap29605-BTA-27618 Hapmap23184-BTC-039909 BTA-23668-no-rs Hapmap23097-BTA161268 BTB-01133499 BTA-26162-no-rs Hapmap55170-rs29017690 Hapmap39910-BTA-30685 BTB-01211463 BTB-01362396 BFGL-NGS-119539 BTA-76842-no-rs Hapmap26729-BTA154447 Hapmap60030-rs29013992

BTB-01069210 Hapmap52732-rs29023384 BTA-88018-no-rs Hapmap53442-rs29021218 BTB-01568097 BTB-01673078

29 6 9 3 4 6

21 3 1 1 2 2

Hapmap60855-rs29024248 Hapmap33628-BTC-041023 Hapmap32210-BTC-035534 Hapmap23862-BTC-069949 Hapmap24317-BTC-037593 Hapmap54823-rs29021261 Hapmap34686BES10_Contig763_1215 Hapmap33922BES7_Contig380_533 BFGL-NGS-116163 BTB-01527594

4 5 7 4 3 6 3

2 6 1 1 2 4 1

3

1

4 6

1 4

BTB-02001974 BTB-02077165 Hapmap23534-BTC-040517 Hapmap39865-BTA-76343 ARS-BFGL-NGS-7689

5 3 10 6 3

1 2 3 2 1

BTA-94706-no-rs BFGL-NGS-114099 ARS-BFGL-NGS-101874 Hapmap51763-BTA-76571 ARS-BFGL-NGS-103013 BTB-01362502 Hapmap52685-rs29017695 BTA-76835-no-rs BTA-114800-no-rs

6 5 6 6 3 4 4 3 4

1 2 1 1 2 1 1 1 2

ARS-BFGL-NGS-80068

3

1

4.45% 0.64% Unique Unique Multiple Multiple Multiple 1.27% Unique Unique Multiple 0.85% Unique Unique Unique 0.85% Unique Multiple 0.64% Multiple Unique Unique Multiple Unique Unique Multiple Unique Unique Unique Multiple Unique

259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286

chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr6 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7

81,354,371 82,226,494 82,558,328 83,023,197 98,421,267 98,735,280 103,508,689 105,348,076 113,870,701 117,437,363 117,809,567 118,460,274 119,339,223 120,303,386 121,859,442 430,234 2,523,562 2,774,563 7,274,494 7,926,601 13,204,650 19,495,494 19,948,893 20,385,996 28,556,469 31,178,692 32,075,728 36,422,388

81,524,194 82,278,023 82,641,003 83,201,479 98,534,076 99,135,154 103,570,611 105,500,024 114,120,926 117,584,429 117,928,864 118,819,518 119,418,044 120,473,416 121,920,646 527,291 2,743,868 2,821,397 7,363,151 8,359,303 13,510,711 19,658,646 20,060,705 20,531,009 28,610,221 31,275,326 32,271,914 36,645,611

169,824 51,530 82,676 178,283 112,810 399,875 61,923 151,949 250,226 147,067 119,298 359,245 78,822 170,031 61,205 97,058 220,307 46,835 88,658 432,703 306,062 163,153 111,813 145,014 53,753 96,635 196,187 223,224

gain gain both loss gain both loss gain both gain gain gain gain gain loss gain gain gain loss gain both gain gain loss gain gain both loss

287 288 289 290 291 292 293


37,078,578 40,664,184 53,858,216 58,354,585 62,197,017 69,342,623 72,962,595

37,274,511 40,797,251 53,907,028 58,561,110 62,525,452 69,438,968 73,142,079

195,934 133,068 48,813 206,526 328,436 96,346 179,485

loss gain gain gain gain gain gain

ARS-BFGL-NGS-108577 BTB-01788388 ARS-BFGL-NGS-13079 BTA-20903-no-rs BTA-29651-no-rs BFGL-NGS-117220 Hapmap27089-BTC-045849 BTB-00275668 BTB-01972609 BTB-00287149 ARS-BFGL-NGS-41285 BFGL-NGS-112242 ARS-BFGL-NGS-56487 ARS-BFGL-NGS-10182 BFGL-NGS-119641 BTB-01218761 Hapmap60952-rs29020997 ARS-BFGL-NGS-14297 ARS-BFGL-NGS-25179 BTB-01778250 ARS-BFGL-NGS-81822 ARS-BFGL-NGS-14152 ARS-BFGL-NGS-29084 BTB-01966013 BFGL-NGS-111972 BTA-116531-no-rs BFGL-NGS-111466 Hapmap48654-BTA121800 BTB-01364448 BTB-00307908 Hapmap52400-rs29025316 BTB-00314357 DIAS-106 ARS-BFGL-NGS-23091 Hapmap50511-BTA-94590

BTB-01393641 Hapmap22939-BTA-149533 Hapmap51938-BTA-21491 BTA-20900-no-rs BTB-01938046 BTB-01965912 Hapmap27088-BTC-045808 Hapmap60824-rs29019638 Hapmap43968-BTA-90824 BTB-02017858 BTA-25280-no-rs ARS-BFGL-NGS-61359 ARS-BFGL-NGS-72209 ARS-BFGL-NGS-59301 ARS-BFGL-NGS-2799 Hapmap47182-BTA-112888 Hapmap49619-BTA-45637 ARS-BFGL-NGS-81715 ARS-BFGL-NGS-81869 ARS-BFGL-NGS-26495 BTA-78357-no-rs UA-IFASA-7694 ARS-BFGL-NGS-13934 Hapmap51514-BTA-88337 ARS-BFGL-NGS-98924 BTA-92602-no-rs Hapmap26699-BTA-147881 ARS-BFGL-NGS-109201

4 3 4 4 4 9 3 4 9 3 6 9 4 6 3 3 8 3 4 10 7 4 3 6 3 3 8 6

1 1 2 1 2 6 1 1 3 1 1 7 1 5 1 1 3 1 1 4 2 1 1 1 1 1 3 1

ARS-BFGL-NGS-26917 BTB-01207097 BFGL-NGS-119198 BTB-01771905 ARS-BFGL-NGS-105590 BTB-00318572 ARS-BFGL-NGS-100614

7 4 3 6 7 4 4

4 1 1 3 11 2 1

Unique Unique Multiple Unique Multiple 1.27% Unique Unique 0.64% Unique Unique 1.48% Unique 1.06% Unique Unique 0.64% Unique Unique 0.85% Multiple Unique Unique Unique Unique Unique 0.64% Unique 0.85% Unique Unique 0.64% 2.33% Multiple Unique

294 295 296 297 298 299 300 301 302 303 304

chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7 chr7

74,122,181 76,490,016 82,149,839 82,529,919 82,728,990 86,300,550 86,744,958 87,003,238 87,864,322 88,185,000 93,401,744

74,306,007 77,443,327 82,283,978 82,669,513 82,867,142 86,554,884 86,905,201 87,203,186 87,975,145 88,302,590 93,534,061

183,827 953,312 134,140 139,595 138,153 254,335 160,244 199,949 110,824 117,591 132,318

both both gain gain gain gain both loss gain loss gain

305 306 307 308 309 310 311 312


101,607,989 103,071,120 104,003,205 105,164,744 105,879,513 109,280,373 4,139,375 4,966,617

101,699,847 103,135,628 104,329,278 105,277,020 105,972,688 109,339,825 4,202,572 5,025,696

91,859 64,509 326,074 112,277 93,176 59,453 63,198 59,080

gain gain gain gain gain loss gain gain

313 314 315 316 317 318 319


9,682,053 14,684,959 15,608,418 20,123,113 21,131,013 21,532,296 22,571,093

9,778,897 14,754,084 15,772,082 20,476,821 21,290,586 21,711,000 22,648,429

96,845 69,126 163,665 353,709 159,574 178,705 77,337

gain gain loss loss loss loss gain

320 321 322 323 324 325 326


25,489,497 26,463,347 32,030,164 32,305,040 33,663,650 34,477,322 35,464,028

25,568,606 26,599,562 32,150,578 32,896,233 33,740,128 34,578,842 35,520,244

79,110 136,216 120,415 591,194 76,479 101,521 56,217

gain gain gain gain gain gain gain

ARS-BFGL-NGS-23727 BTA-98898-no-rs BFGL-NGS-119008 BTA-62449-no-rs Hapmap55579-rs29017355 ARS-BFGL-NGS-3604 BTB-00324587 Hapmap55194-rs29022931 BTA-119020-no-rs BTB-00324071 Hapmap31128-BTA148018 UA-IFASA-6140 BTA-80440-no-rs BTB-00329283 BTB-01671559 ARS-BFGL-NGS-80165 Hapmap45685-BTA-80525 BTA-86030-no-rs Hapmap45337-BTA109277 BTA-44183-no-rs BTA-92138-no-rs BTB-00095218 BFGL-NGS-110231 ARS-BFGL-NGS-4443 BTB-01727300 Hapmap24202-BTA150022 BTB-00733204 BTA-120636-no-rs Hapmap55505-rs29012932 BFGL-NGS-111754 Hapmap54720-rs29023017 BTA-76377-no-rs ARS-BFGL-NGS-1933

ARS-BFGL-NGS-18145 ARS-BFGL-NGS-41030 BTB-00320521 Hapmap53869-rs29020071 Hapmap24347-BTA-158232 BTB-01829004 BTB-00324772 BTB-00325285 BTB-00325898 BTB-01862398 BTA-88250-no-rs

4 18 5 4 5 7 6 7 4 4 5

4 59 1 1 1 2 3 3 3 1 2

BTA-80429-no-rs ARS-BFGL-NGS-94392 BTB-00329036 Hapmap9011-BTA-63465 ARS-BFGL-NGS-92612 Hapmap44412-BTA-80524 BTB-01582726 BTB-01599781

4 3 11 4 4 3 3 3

1 2 5 1 2 1 1 1

BTB-00696278 BTA-85449-no-rs ARS-BFGL-NGS-50811 Hapmap43614-BTA-54308 ARS-BFGL-NGS-54314 BTB-01687547 ARS-BFGL-NGS-29863

4 3 6 7 6 4 3

1 1 1 3 2 1 1

Hapmap52895-rs29012710 BFGL-NGS-114678 BTB-00285279 ARS-BFGL-NGS-99514 BTB-00327358 BTA-76382-no-rs Hapmap23351-BTA-123397

4 5 4 14 4 4 3

1 1 1 1 1 1 1

0.85% 12.50% Unique Unique Unique Multiple 0.64% 0.64% 0.64% Unique Multiple Unique Multiple 1.06% Unique Multiple Unique Unique Unique Unique Unique Unique 0.64% Multiple Unique Unique Unique Unique Unique Unique Unique Unique Unique

327 328 329

chr8 chr8 chr8

36,418,920 36,708,699 37,197,678

36,468,395 36,779,293 37,292,734

49,476 70,595 95,057

loss gain gain

330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345

chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8 chr8

39,075,904 43,752,639 47,862,070 54,970,200 64,005,593 68,112,627 73,731,560 79,342,941 83,001,832 89,202,041 90,019,529 91,843,007 94,538,754 96,209,636 96,931,174 99,892,590

39,184,274 43,885,136 47,926,242 55,062,808 64,139,578 68,323,011 73,850,806 79,435,106 83,181,732 89,575,990 90,218,871 91,886,013 94,732,858 96,281,583 97,601,766 100,005,894

108,371 132,498 64,173 92,609 133,986 210,385 119,247 92,166 179,901 373,950 199,343 43,007 194,105 71,948 670,593 113,305

gain gain gain loss gain gain gain gain gain loss gain loss gain gain both gain

346 347 348 349 350 351 352 353 354 355 356 357 358 359 360


100,799,975 104,885,680 152,679 1,463,199 2,365,513 4,265,260 4,905,205 5,531,752 5,742,333 8,897,451 14,130,039 14,640,139 18,477,636 23,298,098 30,100,532

100,878,878 104,993,059 306,393 1,744,450 2,433,494 4,366,424 5,214,444 5,581,550 6,077,234 8,985,272 14,211,551 14,693,807 18,550,265 23,639,928 30,387,865

78,904 107,380 153,715 281,252 67,982 101,165 309,240 49,799 334,902 87,822 81,513 53,669 72,630 341,831 287,334

gain gain gain gain gain gain gain loss gain loss gain loss loss gain both

BTB-01929442 BTB-01356348 Hapmap41758-BTA116042 BTB-00340836 BTA-20225-no-rs BTB-01679674 BTB-00348080 BTB-00104976 BTA-62442-no-rs BTA-95860-no-rs ARS-BFGL-NGS-89010 BTB-00360597 ARS-BFGL-NGS-20324 BTB-02000008 ARS-BFGL-NGS-4748 BTA-23657-no-rs BTA-16616-no-rs BTB-01363589 Hapmap50244-BTA116790 BTA-102613-no-rs Hapmap58644-rs29010529 BTB-01126890 BTB-01837292 BTB-01697970 BTB-00379107 BTB-01800430 ARS-BFGL-NGS-35259 BTB-01181189 ARS-BFGL-NGS-85616 ARS-BFGL-NGS-78183 BTA-85287-no-rs Hapmap46542-BTA-94412 Hapmap52337-rs29022325 BTB-00386978

BTB-01493310 Hapmap53908-rs29021644 Hapmap59881-rs29018589

3 4 4

1 1 1

BTB-00675470 Hapmap41645-BTA-80995 ARS-BFGL-NGS-83252 BFGL-NGS-111611 BTB-00351490 ARS-BFGL-NGS-53905 BTB-02108039 Hapmap51639-BTA-81812 BTB-00360684 BTB-00301689 BFGL-NGS-116122 UA-IFASA-2827 BTA-23646-no-rs BTB-00488794 BTB-00368155 BTB-01771776

4 4 3 4 5 7 3 3 4 12 6 3 5 3 18 3

5 1 1 1 1 4 3 1 1 1 1 1 2 1 17 1

Hapmap48991-BTA-102596 ARS-BFGL-NGS-74165 BTB-01126874 Hapmap38946-BTA-23689 BTB-01917058 BTA-83564-no-rs BTB-01428058 BTB-01181264 ARS-BFGL-NGS-35242 BFGL-NGS-110800 BTB-01756422 BFGL-NGS-116690 BTA-94407-no-rs ARS-BFGL-NGS-55463 BTB-01218041

3 4 4 5 3 4 8 3 7 3 3 3 3 9 6

1 1 1 3 5 1 12 1 2 1 1 2 1 1 2

Unique Unique Unique 1.06% Unique Unique Unique Unique 0.85% 0.64% Unique Unique Unique Unique Unique Multiple Unique 3.60% Unique Unique Unique Unique 0.64% 1.06% Unique 2.54% Unique Multiple Unique Unique Multiple Unique Unique Multiple

361 362 363 364 365 366 367 368 369


31,230,680 31,568,105 32,421,296 37,851,542 39,465,568 55,904,551 57,142,737 63,467,364 70,014,535

31,370,749 31,757,698 32,543,147 37,986,536 39,653,806 56,005,621 57,954,374 63,513,823 70,056,929

140,070 189,594 121,852 134,995 188,239 101,071 811,638 46,460 42,395

both gain loss loss gain gain loss gain gain

BTA-90733-no-rs BTB-01209657 BTB-01592448 ARS-BFGL-NGS-41040 BTA-83279-no-rs BTA-83723-no-rs BTA-83732-no-rs ARS-BFGL-NGS-10020 ARS-BFGL-NGS-101241

370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395

chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr9 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10 chr10

72,408,821 74,289,845 76,959,628 80,740,460 89,916,177 90,226,974 91,774,408 93,703,893 1,288,074 3,646,693 11,344,781 15,354,740 16,437,277 22,672,607 22,991,034 23,471,955 25,432,120 26,661,443 38,157,709 39,373,018 39,639,943 41,187,571 47,054,697 51,875,050 53,640,116 54,385,812

72,628,414 74,406,044 77,053,824 80,863,324 90,096,917 90,335,703 91,826,221 93,809,495 1,360,039 3,840,464 11,423,079 15,659,184 16,706,426 22,831,437 23,299,956 24,808,294 25,566,607 27,344,970 38,292,369 39,540,553 39,953,528 41,672,043 47,150,297 51,963,015 53,747,496 54,517,057

219,594 116,200 94,197 122,865 180,741 108,730 51,814 105,603 71,966 193,772 78,299 304,445 269,150 158,831 308,923 1,336,340 134,488 683,528 134,661 167,536 313,586 484,473 95,601 87,966 107,381 131,246

loss gain loss gain both gain loss both gain gain gain both loss loss gain gain gain both loss loss gain gain gain both gain gain

Hapmap49339-BTA-84110 ARS-BFGL-NGS-71472 BFGL-NGS-114921 ARS-BFGL-NGS-33739 Hapmap55954-rs29018921 ARS-BFGL-NGS-16116 ARS-BFGL-NGS-63897 BTB-00403355 BTA-07939-rs29027600 ARS-BFGL-NGS-88819 BTB-00411248 BTA-29609-no-rs BFGL-NGS-113265 ARS-BFGL-NGS-100895 BTB-02001051 BTB-01937948 ARS-BFGL-NGS-42815 UA-IFASA-4465 BTA-66227-no-rs BTA-18123-no-rs BTB-00419069 BTB-01400802 ARS-BFGL-NGS-101768 BTB-00992193 BTB-00425665 BTB-01137783

Hapmap51503-BTA-83211 BTB-01444218 BTB-01685265 BTA-86557-no-rs ARS-BFGL-NGS-104555 BTA-17651-no-rs BTB-01346891 ARS-BFGL-NGS-83323 ARS-USMARC-ParentDQ786765-rs29009858 ARS-BFGL-NGS-65921 ARS-BFGL-NGS-40061 ARS-BFGL-NGS-10608 BTA-113455-no-rs BTB-00331176 ARS-BFGL-NGS-54565 BTB-00405268 BTB-00403553 BFGL-NGS-111853 ARS-BFGL-NGS-39354 BTB-01661291 BTB-01490270 ARS-BFGL-NGS-64755 BFGL-NGS-112477 BTB-01703257 BTB-01806171 ARS-BFGL-NGS-97984 BTB-00417555 ARS-BFGL-NGS-102016 BTB-01811042 BTB-00418936 Hapmap51480-BTA-67184 ARS-BFGL-NGS-103937 BTB-00426535 Hapmap57046-rs29017141 Hapmap26429-BTA-150727

3 6 3 5 5 3 23 3 3

2 2 1 1 2 2 2 1 1

3 4 3 3 7 4 3 4 3 5 3 8 7 4 8 19 5 13 4 5 9 13 4 4 4 3

1 1 2 1 26 2 1 2 2 1 1 3 1 2 14 28 1 8 2 1 6 12 1 2 4 1

Multiple Multiple Unique Unique Multiple Multiple Multiple Unique Unique Unique Unique Multiple Unique 5.51% Multiple Unique Multiple Multiple Unique Unique 0.64% Unique Multiple 2.97% 5.93% Unique 1.69% Multiple Unique 1.27% 2.54% Unique Multiple 0.85% Unique

396 397 398 399 400 401 402 403


61,066,582 61,288,405 63,951,124 65,047,747 75,689,938 77,832,357 78,753,759 80,601,154

61,165,187 61,379,612 64,041,482 65,159,485 75,872,732 77,927,864 78,870,385 80,696,497

98,606 91,208 90,359 111,739 182,795 95,508 116,627 95,344

gain gain gain gain loss loss gain gain

404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426

chr10 chr10 chr10 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11 chr11

87,942,523 91,525,897 96,508,075 8,998,918 12,403,533 19,657,413 24,949,976 35,183,063 35,630,220 40,028,208 41,363,787 52,793,421 59,350,663 60,102,402 61,027,589 62,063,297 63,556,147 71,449,884 86,227,752 90,676,507 90,823,124 91,819,727 92,923,848

88,017,740 91,578,510 96,582,302 9,105,655 12,634,068 19,759,923 25,076,271 35,359,692 35,716,272 40,164,558 41,486,028 53,000,095 59,498,037 60,242,004 61,558,407 62,121,579 63,640,435 71,571,653 86,271,659 90,730,972 90,889,956 91,877,383 93,023,361

75,218 52,614 74,228 106,738 230,536 102,511 126,296 176,630 86,053 136,351 122,242 206,675 147,375 139,603 530,819 58,283 84,289 121,770 43,908 54,466 66,833 57,657 99,514

loss gain loss gain both both gain loss gain loss gain gain loss both loss gain gain gain gain gain gain loss loss

427 428 429

chr11 chr11 chr11

96,616,167 101,355,330 103,644,699

96,687,307 101,473,846 103,711,868

71,141 118,517 67,170

gain loss gain

BTB-01361809 Hapmap50139-BTA-87645 BTB-00432722 BTA-73355-no-rs ARS-BFGL-BAC-7172 Hapmap51491-BTA-75258 Hapmap60368-rs29015590 Hapmap24868-BTA156007 BTB-00441700 BTA-79335-no-rs BTA-15736-no-rs ARS-BFGL-NGS-28887 ARS-BFGL-BAC-13566 BTA-118292-no-rs BTB-01444868 BTB-01641061 BTA-92800-no-rs Hapmap51861-BTA-86131 Hapmap44496-BTA-91437 ARS-BFGL-NGS-66467 Hapmap60711-rs29014674 BTA-34561-no-rs Hapmap59738-rs29016857 Hapmap53164-rs29012136 ARS-BFGL-BAC-13039 ARS-BFGL-NGS-30983 ARS-BFGL-NGS-63978 ARS-BFGL-NGS-107179 ARS-BFGL-NGS-37074 ARS-BFGL-NGS-83535 Hapmap39886-BTA112449 BTB-02006984 ARS-BFGL-NGS-5179 ARS-BFGL-NGS-38345

BTA-66849-no-rs Hapmap44561-BTA-72345 ARS-BFGL-NGS-80176 BTA-73359-no-rs ARS-BFGL-NGS-69839 BFGL-NGS-116801 Hapmap27859-BTA-125757 ARS-BFGL-NGS-55923

4 4 3 3 7 3 3 3

2 3 1 2 1 1 3 6

BTB-00441734 BFGL-NGS-119578 Hapmap59536-rs29025348 Hapmap46925-BTA-108435 BTA-85491-no-rs BTA-88187-no-rs BTB-01374666 Hapmap44196-BTA-113212 BTB-01293391 Hapmap47774-BTA-89811 Hapmap27268-BTA-91439 ARS-BFGL-NGS-26558 BTB-01328920 ARS-BFGL-BAC-11747 BTB-01652151 Hapmap32846-BTA-152118 Hapmap29025-BTA-156546 BFGL-NGS-110913 Hapmap40163-BTA-107343 BFGL-NGS-114352 ARS-BFGL-NGS-25119 ARS-BFGL-NGS-39719 BFGL-NGS-114789

4 3 4 5 4 4 4 3 4 4 4 3 3 5 11 3 3 5 3 3 4 3 4

1 2 1 1 2 2 1 1 1 1 1 1 1 7 1 1 2 1 1 1 1 2 1

BTA-114544-no-rs BFGL-NGS-114759 ARS-BFGL-NGS-14427

3 5 3

1 1 1

Multiple 0.64% Unique Multiple Unique Unique 0.64% 1.27% Unique Multiple Unique Unique Multiple Multiple Unique Unique Unique Unique Unique Unique Unique 1.48% Unique Unique Multiple Unique Unique Unique Unique Multiple Unique Unique Unique Unique

430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445

chr11 chr11 chr11 chr11 chr11 chr11 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12 chr12

104,056,769 107,470,735 107,916,725 108,197,801 108,616,362 110,100,672 1,542,501 2,453,428 3,779,257 7,097,688 7,596,510 8,378,704 9,662,952 10,107,160 10,264,902 25,884,193

104,158,798 107,650,972 108,119,253 108,480,494 109,555,306 110,171,705 1,627,266 2,734,960 3,940,304 7,181,723 7,777,259 8,475,144 9,736,235 10,161,530 10,436,001 26,132,031

102,030 180,238 202,529 282,694 938,945 71,034 84,766 281,533 161,048 84,036 180,750 96,441 73,284 54,371 171,100 247,839

gain gain gain both both gain gain loss gain gain loss gain gain loss loss gain

446 447 448 449 450 451 452 453 454


35,180,525 40,071,934 44,796,637 45,562,272 53,433,901 56,072,810 56,278,598 56,704,809 57,219,963

35,349,285 40,219,700 45,202,694 45,707,966 53,593,829 56,146,422 56,358,272 56,842,321 57,946,286

168,761 147,767 406,058 145,695 159,929 73,613 79,675 137,513 726,324

gain gain both both loss gain loss gain both

ARS-BFGL-NGS-11554 ARS-BFGL-NGS-9222 ARS-BFGL-NGS-29433 ARS-BFGL-NGS-4101 ARS-BFGL-NGS-35143 ARS-BFGL-NGS-17264 BTA-102244-no-rs BTA-87244-no-rs ARS-BFGL-NGS-10688 ARS-BFGL-BAC-15052 Hapmap38662-BTA-22753 BTA-53873-no-rs ARS-BFGL-NGS-31596 Hapmap43230-BTA-31437 ARS-BFGL-NGS-55319 Hapmap27862-BTA127450 ARS-BFGL-NGS-28809 BTA-102528-no-rs BTA-21671-no-rs Hapmap44038-BTA-22707 BTB-00221770 BTB-01021031 BTA-65462-no-rs BTB-01834845 BTB-02035517

455 456 457 458 459 460 461 462 463


58,705,245 61,210,425 62,502,265 63,653,956 66,828,057 67,211,913 69,013,308 69,888,102 71,126,819

58,764,780 61,303,732 62,790,151 64,166,118 66,907,342 67,279,643 69,599,639 70,511,189 71,172,102

59,536 93,308 287,887 512,163 79,286 67,731 586,332 623,088 45,284

gain loss gain both gain loss both both loss

BTB-00506214 BTB-01625209 BTB-01507160 BFGL-NGS-110053 BTB-01116037 BTA-27027-no-rs ARS-BFGL-NGS-45730 BTB-02031101 ARS-BFGL-NGS-85162

BFGL-NGS-114241 BFGL-NGS-114744 BFGL-NGS-116393 ARS-BFGL-NGS-82419 ARS-BFGL-NGS-100593 ARS-BFGL-NGS-34624 ARS-BFGL-NGS-75777 BFGL-NGS-111874 Hapmap48714-BTA-31352 BTA-26945-no-rs BTB-00486335 BTB-01665706 Hapmap22720-BTA-24775 BFGL-NGS-119608 UA-IFASA-4065 Hapmap24457-BTA-153392

3 6 7 9 22 4 3 10 4 3 6 3 3 3 8 5

1 1 2 2 13 1 1 1 5 2 2 1 1 1 1 1

Hapmap59507-rs29021330 Hapmap47157-BTA-102522 BTB-01438513 ARS-BFGL-NGS-45919 BTB-00496106 BTB-01021085 ARS-BFGL-NGS-20125 BTB-00499591 Hapmap33957BES4_Contig323_1373 BTB-00506165 Hapmap51863-BTA-89179 BTB-01713461 ARS-BFGL-NGS-10953 BTB-00501374 BTB-00500819 BTA-95991-no-rs ARS-BFGL-NGS-77009 ARS-BFGL-NGS-84920

5 4 13 5 6 4 4 5 21

6 1 7 10 2 1 1 1 23

3 3 8 12 4 3 11 16 3

1 1 9 3 1 1 90 74 1

Unique Unique Multiple Multiple 2.75% Unique Unique Unique 1.06% Multiple Multiple Unique Unique Unique Unique Unique 1.27% Unique 1.48% 2.12% Multiple Unique Unique Unique 4.87% Unique Unique 1.91% 0.64% Unique Unique 19.07% 15.68% Unique

464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499

chr12 chr12 chr12 chr12 chr12 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr13 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14

73,940,304 74,184,495 75,808,866 78,681,039 84,428,478 679,675 3,482,936 9,756,821 16,458,536 19,304,187 20,815,498 21,438,875 37,651,429 40,615,728 51,003,729 53,898,041 55,587,021 61,619,059 62,497,133 63,184,085 70,641,477 80,091,357 2,763,656 5,196,948 12,958,060 18,004,867 25,288,715 30,329,983 32,545,419 36,054,987 46,274,447 46,791,102 48,395,915 49,329,524 51,352,709 51,668,755

74,013,793 74,371,680 75,885,294 78,742,005 84,561,131 781,641 3,674,685 9,901,248 16,924,591 19,604,000 20,921,843 21,573,213 37,721,330 40,974,988 51,065,386 54,215,079 55,716,110 61,784,382 62,824,358 63,259,211 70,718,468 80,419,471 2,849,482 5,318,260 13,296,381 18,190,755 25,566,835 30,404,140 32,854,553 36,467,315 46,354,991 47,573,138 48,752,330 49,577,713 51,548,386 51,817,937

73,490 187,186 76,429 60,967 132,654 101,967 191,750 144,428 466,056 299,814 106,346 134,339 69,902 359,261 61,658 317,039 129,090 165,324 327,226 75,127 76,992 328,115 85,827 121,313 338,322 185,889 278,121 74,158 309,135 412,329 80,545 782,037 356,416 248,190 195,678 149,183

gain gain gain gain gain loss both gain gain both gain gain gain gain loss gain both loss both loss gain gain loss loss both gain loss gain both loss gain both both both both loss

ARS-BFGL-NGS-100 Hapmap58260-rs29024773 ARS-BFGL-NGS-2850 Hapmap50653-BTA-31308 ARS-BFGL-NGS-36097 BTB-01141508 ARS-BFGL-NGS-4272 BTA-93505-no-rs ARS-BFGL-BAC-7407 BTA-90541-no-rs Hapmap51705-BTA-24478 Hapmap42135-BTA-21541 ARS-BFGL-NGS-26566 ARS-BFGL-NGS-37354 BTA-92697-no-rs BFGL-NGS-110706 ARS-BFGL-NGS-68008 Hapmap60926-rs29018487 Hapmap43021-BTA-71454 ARS-BFGL-NGS-90718 ARS-BFGL-NGS-35840 BFGL-NGS-112395 UA-IFASA-5765 Hapmap26023-BTC-049737 BFGL-NGS-119174 BTB-01720493 Hapmap27934-BTC-065223 UA-IFASA-7790 BFGL-NGS-112227 UA-IFASA-6272 UA-IFASA-6664 BTB-01891955 BTA-34930-no-rs Hapmap39850-BTA-60175 Hapmap27678-BTC-012488 Hapmap33279-BTC-012214

ARS-BFGL-NGS-36295 Hapmap40904-BTA-120929 BTA-87771-no-rs BTA-31315-no-rs ARS-BFGL-NGS-23827 Hapmap26161-BTA-151057 Hapmap46901-BTA-05645 BTA-61986-no-rs Hapmap39401-BTA-34229 BTB-01233700 ARS-BFGL-NGS-103700 ARS-BFGL-NGS-72802 ARS-BFGL-NGS-88501 BFGL-NGS-116093 Hapmap60983-rs29011505 BTA-25036-no-rs ARS-BFGL-NGS-22427 Hapmap49573-BTA-33131 ARS-BFGL-NGS-104301 ARS-BFGL-NGS-100677 BTA-120959-no-rs BFGL-NGS-119925 ARS-BFGL-NGS-84713 Hapmap33635-BTC-049051 ARS-BFGL-NGS-93639 BTB-01283269 Hapmap23456-BTC-072918 UA-IFASA-6771 UA-IFASA-7535 BTB-00983525 BTB-01223219 Hapmap43763-BTA-111412 BTB-00570934 Hapmap44105-BTA-60185 Hapmap31256-BTC-012280 Hapmap27809-BTC-001663

3 5 3 3 4 3 6 3 12 8 4 3 3 9 3 6 5 4 8 4 3 11 5 5 12 5 10 3 7 9 3 18 10 7 9 6

1 1 1 2 1 1 2 3 19 3 1 1 2 1 1 3 2 1 4 1 1 3 1 1 30 3 2 1 2 2 1 15 4 7 4 3

Unique Unique Unique Multiple Unique Unique Multiple 0.64% 4.03% 0.64% Unique Unique Multiple Unique Unique 0.64% Multiple Unique 0.85% Unique Unique 0.64% Unique Unique 6.36% 0.64% Multiple Unique Multiple Multiple Unique 3.18% 0.85% 1.48% 0.85% 0.64%

500 501 502 503 504 505 506 507 508 509 510 511

chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr14 chr15 chr15 chr15

51,959,707 52,432,837 58,301,732 59,446,097 64,527,567 68,856,411 72,257,437 73,547,229 74,472,888 4,416,208 5,242,765 5,437,080

52,047,098 52,576,338 58,389,113 59,584,308 64,742,565 69,036,295 72,346,742 73,935,209 74,548,770 4,548,728 5,324,917 5,636,828

87,392 143,502 87,382 138,212 214,999 179,885 89,306 387,981 75,883 132,521 82,153 199,749

gain gain gain gain gain gain gain gain gain gain loss both

512 513 514 515 516


6,585,863 7,433,807 7,997,896 9,138,221 10,136,876

6,708,080 7,592,643 8,385,314 9,581,859 10,301,216

122,218 158,837 387,419 443,639 164,341

gain loss both both gain

Hapmap22896-BTC-012573 Hapmap26251-BTC-013832 BTA-110835-no-rs BTB-00575420 ARS-BFGL-NGS-59595 Hapmap55935-rs29020117 ARS-BFGL-NGS-33113 BTA-116518-no-rs BTB-00576713 BTA-55622-no-rs BTB-01713978 Hapmap28179-BTA149370 BTB-02089263 BTA-91114-no-rs ARS-BFGL-NGS-48673 BTA-96456-no-rs BTB-01384592

517 518 519 520 521 522 523


12,331,424 12,813,466 14,632,044 15,767,956 18,425,342 20,330,102 29,442,486

12,450,750 12,870,679 14,729,248 15,982,903 18,646,489 20,415,439 29,677,744

119,327 57,214 97,205 214,948 221,148 85,338 235,259

gain gain gain gain both gain both

ARS-BFGL-BAC-19445 BTA-93194-no-rs BTA-121003-no-rs ARS-BFGL-NGS-17853 ARS-BFGL-NGS-80166 BTA-99633-no-rs BTA-36278-no-rs

524 525 526 527 528 529 530 531 532


32,573,953 32,971,747 35,749,606 41,284,039 43,199,892 45,205,017 48,939,595 50,905,152 53,109,622

32,699,764 33,077,359 36,005,328 41,351,115 43,310,531 45,268,074 49,384,451 50,954,601 53,245,381

125,812 105,613 255,723 67,077 110,640 63,058 444,857 49,450 135,760

gain gain both loss gain gain both gain gain

ARS-BFGL-NGS-17345 UA-IFASA-8490 BFGL-NGS-112089 ARS-BFGL-NGS-41246 BTA-90079-no-rs BTB-00599630 BTB-01501127 UA-IFASA-8473 Hapmap35699-

Hapmap32919-BTC-012734 ARS-BFGL-NGS-35964 ARS-BFGL-NGS-1405 ARS-BFGL-NGS-108994 ARS-BFGL-NGS-31720 ARS-BFGL-NGS-12011 BTA-35507-no-rs ARS-BFGL-NGS-104297 UA-IFASA-6716 BTB-00578401 BTB-00580383 ARS-BFGL-NGS-22440

4 6 3 4 6 6 3 8 3 4 3 4

1 1 1 1 1 11 2 1 1 1 1 2

ARS-BFGL-NGS-56415 BTB-01173692 BTB-00580638 BTA-94770-no-rs ARS-USMARC-ParentEF042090-no-rs ARS-BFGL-BAC-19446 BFGL-NGS-110213 Hapmap44541-BTA-37632 BTA-99296-no-rs BTA-05407-rs29019567 BTB-01820462 Hapmap36165SCAFFOLD12487_317 ARS-BFGL-NGS-26086 BTA-123344-no-rs BFGL-NGS-110172 ARS-BFGL-NGS-25667 ARS-BFGL-NGS-107315 BFGL-NGS-115713 BTB-01917542 ARS-BFGL-NGS-31942 ARS-BFGL-BAC-2207

3 4 7 8 5

1 1 13 25 3

3 3 3 3 7 3 7

1 1 1 1 8 1 7

4 4 9 4 4 3 6 3 4

1 1 4 1 1 1 7 3 1

Unique Unique Unique Unique Unique 2.33% Multiple Unique Unique Unique Unique Multiple Unique Unique 2.75% 5.30% 0.64% Unique Unique Unique Unique 1.69% Unique 1.48% Unique Unique 0.85% Unique Unique Unique 1.48% 0.64% Unique

533 534 535

chr15 chr15 chr15

56,050,568 56,280,210 56,777,644

56,123,313 56,557,487 56,889,858

72,746 277,278 112,215

loss both loss

536 537 538 539 540 541 542 543 544 545 546 547

chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15 chr15

57,473,959 58,438,839 61,264,456 62,431,809 64,280,181 67,988,356 68,481,032 69,898,109 70,221,593 77,893,601 78,764,623 79,934,410

57,543,255 58,655,770 61,390,135 62,534,879 64,349,074 68,345,442 68,704,512 69,995,636 70,405,931 78,342,209 79,191,195 80,256,966

69,297 216,932 125,680 103,071 68,894 357,087 223,481 97,528 184,339 448,609 426,573 322,557

gain both gain gain loss both both loss gain gain gain both

548 549 550 551 552 553 554 555 556


83,221,355 246,311 534,509 3,970,643 4,553,016 7,356,282 8,023,375 8,195,478 8,972,958

83,434,168 361,734 789,249 4,058,551 4,718,732 7,408,352 8,135,362 8,334,137 9,042,654

212,814 115,424 254,741 87,909 165,717 52,071 111,988 138,660 69,697

gain gain gain gain loss gain gain both loss

557 558 559

chr16 chr16 chr16

9,583,852 14,267,595 15,240,447

9,656,456 14,442,044 15,353,483

72,605 174,450 113,037

gain both gain

560 561 562 563

chr16 chr16 chr16 chr16

17,361,387 18,368,967 24,999,357 25,823,223

17,461,759 18,500,742 25,069,065 25,996,326

100,373 131,776 69,709 173,104

loss gain gain gain

UCP3_119F1-SNP1 ARS-BFGL-NGS-12085 ARS-BFGL-BAC-19997 Hapmap27950-BTA130038 ARS-BFGL-NGS-64353 BTB-00608455 BFGL-NGS-112085 ARS-BFGL-NGS-63905 ARS-BFGL-NGS-59477 BTB-01279265 ARS-BFGL-NGS-26597 BTB-01010030 BTB-01997082 BTB-00618478 BTB-01749101 Hapmap33180-BTA119730 ARS-BFGL-NGS-31313 ARS-BFGL-NGS-3398 Hapmap40528-BTA-38570 ARS-BFGL-NGS-54578 BTA-109095-no-rs BTB-00228319 BTB-00628142 Hapmap49982-BTA-39672 Hapmap33576-BTA130425 BTA-118128-no-rs BTA-91807-no-rs Hapmap23394-BTA130434 BFGL-NGS-112624 ARS-BFGL-NGS-60500 BTA-114494-no-rs Hapmap48735-BTA-38349

ARS-BFGL-NGS-27017 ARS-BFGL-BAC-19991 Hapmap39958-BTA-96258

4 10 5

1 23 1

DIAS-217 BTB-01561003 BTA-105181-no-rs BTB-01280617 BTA-37293-no-rs BTB-00612553 BTB-00613090 BTB-00614284 BTB-00613588 UA-IFASA-5162 BTB-02093045 ARS-BFGL-NGS-76982

3 5 3 4 3 10 7 4 6 12 10 10

1 3 2 1 1 8 6 1 1 3 9 82

BTB-02014893 BFGL-NGS-110500 BTB-01324160 BTB-01885608 Hapmap33722-BTA-155362 BTB-01222074 ARS-BFGL-NGS-83817 Hapmap43811-BTA-22208 BTB-01533537

5 5 8 3 5 3 5 6 3

33 1 1 1 3 1 5 3 1

BTA-29787-no-rs ARS-BFGL-BAC-20631 BTB-01113828

3 6 4

7 2 2

ARS-BFGL-NGS-6876 ARS-BFGL-NGS-55834 BTA-61271-no-rs ARS-BFGL-NGS-42514

3 4 3 6

1 1 2 2

Unique 4.87% Unique Unique 0.64% Multiple Unique Unique 1.69% 1.27% Unique Unique 0.64% 1.91% 17.37% 6.99% Unique Unique Unique 0.64% Unique 1.06% 0.64% Unique 1.48% Multiple Multiple Unique Unique Multiple Multiple

564 565 566 567 568


26,041,123 27,161,003 32,451,419 43,358,415 46,299,669

26,314,168 27,265,035 32,516,642 43,418,277 46,492,210

273,046 104,033 65,224 59,863 192,542

gain both loss gain gain

Hapmap44646-BTA-38361 BTB-01274565 Hapmap45766-BTA-38696 BTB-00642704 BTB-01842164

569 570 571 572 573 574 575 576 577


46,748,926 48,016,530 54,755,641 68,351,701 75,867,294 995,320 1,905,934 2,314,496 7,074,359

46,940,788 48,117,007 55,031,619 68,464,242 75,926,053 1,050,809 2,009,477 2,446,766 7,158,917

191,863 100,478 275,979 112,542 58,760 55,490 103,544 132,271 84,559

gain gain both loss both gain gain gain gain

578 579 580

chr17 chr17 chr17

11,394,641 12,506,471 19,895,917

11,618,576 12,619,659 19,983,638

223,936 113,189 87,722

gain loss loss

Hapmap58832-rs29018603 BTB-00646081 ARS-BFGL-BAC-34694 BTB-00659445 Hapmap39526-BTA-95520 BTB-02009238 BTB-01855576 ARS-BFGL-NGS-101175 Hapmap36186SCAFFOLD206949_1268 Hapmap40124-BTA-42067 BTB-00671456 Hapmap51224-BTA-40595

581 582 583 584 585 586


24,123,879 37,718,709 41,104,253 43,229,127 43,749,738 44,876,575

24,727,631 37,778,234 41,211,910 43,485,249 43,877,477 44,971,455

603,753 59,526 107,658 256,123 127,740 94,881

both loss both gain loss loss

587 588 589 590 591 592


56,648,121 64,563,142 65,288,848 66,067,477 69,440,276 71,389,254

56,899,149 64,689,649 65,408,860 66,128,855 69,604,943 71,531,747

251,029 126,508 120,013 61,379 164,668 142,494

gain gain gain loss loss gain

593 594 595

chr17 chr17 chr18

74,239,622 75,490,898 1,818,245

74,639,933 76,487,768 1,981,291

400,312 996,871 163,047

both both gain

ARS-BFGL-BAC-35969 Hapmap49526-BTA-20762 ARS-BFGL-BAC-32745 BTB-01620081 Hapmap42485-BTA-25566 Hapmap26742-BTA156593 BFGL-NGS-111753 Hapmap60900-rs29022475 ARS-BFGL-NGS-50172 BTB-01998842 ARS-BFGL-NGS-23383 Hapmap27966-BTA149885 ARS-BFGL-NGS-105203 Hapmap49164-BTA-42015 ARS-BFGL-NGS-103061

ARS-BFGL-BAC-33363 BTA-16289-no-rs ARS-BFGL-NGS-15956 BTA-38976-no-rs ARS-USMARC-ParentAY857620-rs17871214 ARS-BFGL-NGS-32187 ARS-BFGL-NGS-18487 Hapmap49101-BTA-26374 Hapmap48745-BTA-40019 ARS-BFGL-NGS-100673 BTA-100586-no-rs ARS-BFGL-NGS-28768 BTB-01727358 BTB-00670110

6 5 3 3 7

4 2 1 3 2

7 4 7 3 3 3 3 4 3

2 1 3 1 2 1 1 1 1

BTA-87167-no-rs Hapmap52434-rs29012066 ARS-USMARC-ParentAY858890-rs29002256 BTA-88834-no-rs Hapmap59822-rs29020659 Hapmap44543-BTA-40914 BTB-01759971 BTB-01282074 BTA-113152-no-rs

7 4 4

1 1 2

14 3 4 6 4 3

9 1 8 4 1 1

Hapmap33195-BTA-131536 ARS-BFGL-NGS-29331 BTB-00684402 ARS-BFGL-NGS-13866 ARS-BFGL-NGS-66134 ARS-BFGL-NGS-103734

6 3 4 3 4 3

1 1 3 1 1 1

ARS-BFGL-NGS-38439 ARS-BFGL-NGS-35060 Hapmap56936-ss46526655

13 32 3

12 22 1

0.85% Multiple Unique 0.64% Multiple Multiple Unique 0.64% Unique Multiple Unique Unique Unique Unique Unique Unique Multiple 1.91% Unique 1.69% 0.85% Unique Unique Unique Unique 0.64% Unique Unique Unique 2.54% 4.66% Unique

596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631

chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr18 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr19 chr20 chr20 chr20

13,260,824 13,729,245 14,741,765 18,885,794 20,491,863 20,977,959 21,689,813 34,866,810 37,223,671 37,776,086 40,280,913 44,010,754 48,012,475 50,276,514 51,920,266 54,489,550 57,155,997 59,413,220 60,324,014 61,095,494 61,209,053 62,342,013 63,874,985 4,319,527 6,155,199 12,551,500 27,103,596 29,938,951 55,369,288 57,620,657 58,469,747 63,578,439 64,763,344 1,262,421 4,622,895 6,007,890

13,360,139 13,864,212 14,906,639 18,987,405 20,610,059 21,098,149 21,787,052 34,934,949 37,321,698 38,051,481 40,362,735 44,081,244 48,223,045 50,537,220 52,013,918 54,632,111 57,306,049 59,762,913 60,560,946 61,176,289 61,607,122 62,456,233 63,981,698 4,526,189 6,381,628 12,611,334 27,236,623 30,185,040 55,477,012 57,667,589 58,596,190 63,651,365 64,977,290 1,312,760 4,669,000 6,051,949

99,316 134,968 164,875 101,612 118,197 120,191 97,240 68,140 98,028 275,396 81,823 70,491 210,571 260,707 93,653 142,562 150,053 349,694 236,933 80,796 398,070 114,221 106,714 206,663 226,430 59,835 133,028 246,090 107,725 46,933 126,444 72,927 213,947 50,340 46,106 44,060

gain gain gain loss gain gain gain loss gain gain gain gain gain gain gain gain gain gain gain gain gain gain gain gain gain loss gain gain gain gain gain loss loss gain gain loss

ARS-BFGL-NGS-107284 ARS-BFGL-NGS-2774 BTB-00702434 Hapmap48245-BTA-20441 BTB-00705849 Hapmap51594-BTA-42721 Hapmap49169-BTA-42663 BFGL-NGS-113568 ARS-BFGL-NGS-94389 Hapmap58822-rs29018153 ARS-BFGL-NGS-37079 Hapmap40732-BTA-43433 UA-IFASA-6796 ARS-BFGL-NGS-12344 BFGL-NGS-112862 ARS-BFGL-NGS-101147 BTA-43976-no-rs BTB-01439818 ARS-BFGL-NGS-100326 ARS-BFGL-NGS-21704 ARS-BFGL-NGS-49873 ARS-BFGL-NGS-34007 BTB-01399514 Hapmap49106-BTA-28140 ARS-BFGL-BAC-32502 ARS-BFGL-NGS-99672 BFGL-NGS-113401 Hapmap39407-BTA-45009 ARS-BFGL-NGS-71901 BFGL-NGS-114597 BFGL-NGS-115627 UA-IFASA-9390 ARS-BFGL-NGS-100441 ARS-BFGL-NGS-23593 ARS-BFGL-NGS-48030 ARS-BFGL-NGS-5145

Hapmap44238-BTA-42338 ARS-BFGL-NGS-32064 Hapmap55003-rs29021758 Hapmap44501-BTA-94662 BTA-123174-no-rs BTA-42733-no-rs ARS-BFGL-NGS-77651 ARS-BFGL-NGS-52078 Hapmap48151-BTA-101548 Hapmap24078-BTA-132268 ARS-BFGL-NGS-67853 BTA-11776-rs29017530 ARS-BFGL-NGS-22956 ARS-BFGL-BAC-28003 BTA-77181-no-rs ARS-BFGL-NGS-70161 ARS-BFGL-NGS-15079 BTB-01915799 BTB-01457823 ARS-BFGL-NGS-14613 BFGL-NGS-110828 ARS-BFGL-NGS-25758 BFGL-NGS-110088 BFGL-NGS-114249 UA-IFASA-8401 ARS-BFGL-NGS-101517 ARS-BFGL-NGS-37715 ARS-BFGL-NGS-8442 ARS-BFGL-NGS-105050 ARS-BFGL-NGS-29163 ARS-BFGL-NGS-34845 UA-IFASA-9580 ARS-BFGL-NGS-101228 ARS-BFGL-NGS-8109 ARS-BFGL-NGS-25266 Hapmap48214-BTA-121272

3 3 4 4 3 3 3 3 3 7 3 3 4 4 3 4 6 4 5 4 9 4 4 5 6 3 4 8 4 3 3 3 6 3 3 3

1 1 3 2 1 1 1 1 3 2 2 1 1 1 1 4 18 1 1 1 19 1 1 7 1 1 1 1 2 1 1 1 1 1 1 1

Unique Unique 0.64% Multiple Unique Unique Unique Unique 0.64% Multiple Multiple Unique Unique Unique Unique 0.85% 3.81% Unique Unique Unique 4.03% Unique Unique 1.48% Unique Unique Unique Unique Multiple Unique Unique Unique Unique Unique Unique Unique

632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655

chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr20 chr21 chr21 chr21 chr21

6,555,725 17,820,230 19,771,943 27,625,905 30,407,374 45,547,099 47,105,778 48,702,761 49,510,403 50,450,690 51,402,609 52,263,554 52,496,422 52,937,410 54,301,836 55,385,094 56,494,412 56,965,211 57,799,684 75,023,691 822,328 3,149,018 10,922,512 14,625,807

6,686,404 17,955,243 19,856,633 27,736,999 30,566,515 46,767,627 47,203,067 48,948,264 49,716,158 50,564,369 51,459,233 52,347,293 52,581,528 53,290,555 54,534,059 55,600,901 56,783,945 57,408,215 57,985,975 75,147,654 866,253 3,298,809 11,102,542 14,725,723

130,680 135,014 84,691 111,095 159,142 1,220,529 97,290 245,504 205,756 113,680 56,625 83,740 85,107 353,146 232,224 215,808 289,534 443,005 186,292 123,964 43,926 149,792 180,031 99,917

loss loss loss loss gain both loss both both loss gain loss loss gain loss gain loss both loss gain gain gain gain gain

656 657 658 659 660 661 662 663 664 665 666

chr21 chr21 chr21 chr21 chr21 chr21 chr21 chr21 chr21 chr21 chr21

16,638,720 16,859,168 18,263,962 23,223,602 25,025,436 27,559,279 30,285,127 31,479,521 34,322,953 36,082,595 36,837,821

16,686,928 16,913,324 18,449,899 23,366,241 25,183,862 27,747,438 30,346,881 31,529,569 34,415,517 36,295,258 36,994,970

48,209 54,157 185,938 142,640 158,427 188,160 61,755 50,049 92,565 212,664 157,150

gain gain gain gain gain gain gain gain loss gain loss

BFGL-NGS-118422 Hapmap48788-BTA-49979 ARS-BFGL-BAC-33645 ARS-BFGL-NGS-107036 BTA-50169-no-rs Hapmap54108-rs29011104 BTB-00784875 BTB-00786292 Hapmap39563-BTA-41519 ARS-BFGL-BAC-32364 Hapmap61086-rs29010403 BTB-01953992 ARS-BFGL-BAC-32381 BTB-01298102 BTB-00787214 BTB-01132101 BTB-00787949 BTA-50817-no-rs BTA-89573-no-rs ARS-BFGL-BAC-31783 ARS-BFGL-NGS-18147 ARS-BFGL-NGS-18711 BTA-12959-no-rs Hapmap35433SCAFFOLD255531_13677 DIAS-242 BTA-117498-no-rs BFGL-NGS-116442 ARS-BFGL-NGS-3776 ARS-BFGL-NGS-75748 ARS-BFGL-NGS-102263 ARS-BFGL-NGS-37012 ARS-BFGL-NGS-101477 BFGL-NGS-114625 Hapmap41286-BTA-52147 BTB-01303836

ARS-BFGL-NGS-105013 BFGL-NGS-114288 BTA-115951-no-rs ARS-BFGL-NGS-109046 ARS-BFGL-NGS-10984 BTB-01441573 BTA-50669-no-rs ARS-BFGL-BAC-32350 ARS-BFGL-BAC-32355 Hapmap54884-rs29017180 Hapmap61109-rs29012067 BTB-01522825 BTB-02087263 BTA-111516-no-rs Hapmap52570-rs29024651 ARS-BFGL-NGS-80731 ARS-BFGL-NGS-21193 BTA-00660-no-rs BTB-01128234 ARS-BFGL-NGS-23012 ARS-BFGL-NGS-92774 Hapmap51927-BTA-105778 BFGL-NGS-116037 ARS-BFGL-NGS-100582

5 4 3 3 3 29 4 8 7 4 3 3 3 4 6 4 6 11 6 6 3 6 4 4

1 1 1 1 1 60 1 8 16 1 1 1 1 2 1 1 1 2 3 2 1 1 1 4

Hapmap49643-BTA-51662 BTB-01769597 ARS-BFGL-BAC-32705 Hapmap25623-BTA-162140 BFGL-NGS-119582 BTB-01176930 BFGL-NGS-117989 BFGL-NGS-119025 ARS-BFGL-NGS-58606 Hapmap58716-rs29021182 BTB-01303818

3 3 7 4 5 6 3 3 3 5 4

2 1 1 1 1 1 1 1 1 1 7

Unique Unique Unique Unique Unique 12.71% Unique 1.69% 3.39% Unique Unique Unique Unique Multiple Unique Unique Unique Multiple 0.64% Multiple Unique Unique Unique 0.85% Multiple Unique Unique Unique Unique Unique Unique Unique Unique Unique 1.48%

667 668 669 670 671 672 673


38,570,316 39,107,274 40,025,946 40,908,072 43,174,463 44,671,100 52,001,250

38,698,584 39,185,841 40,140,982 40,990,926 43,258,485 44,946,634 52,064,649

128,269 78,568 115,037 82,855 84,023 275,535 63,400

loss gain loss gain gain both gain

674 675 676 677 678 679 680 681


59,453,462 61,004,967 63,588,699 69,029,934 4,942,115 5,325,046 9,765,905 16,025,803

59,534,330 61,053,124 63,699,750 69,171,298 5,074,899 5,588,639 10,388,191 16,089,257

80,869 48,158 111,052 141,365 132,785 263,594 622,287 63,455

gain gain loss gain gain gain gain gain

682 683 684 685

chr22 chr22 chr22 chr22

19,879,037 22,662,782 25,862,468 27,912,159

20,093,810 23,032,569 26,139,335 27,994,848

214,774 369,788 276,868 82,690

both gain gain gain

686 687

chr22 chr22

28,029,558 37,193,844

28,137,454 37,328,687

107,897 134,844

loss gain

688

chr22

39,797,272

39,853,554

56,283

gain

689 690 691 692 693 694 695 696 697


41,623,070 49,824,948 52,629,779 60,300,958 61,117,993 61,644,161 1,829,364 2,191,306 5,649,169

41,680,974 49,976,875 52,800,409 60,619,340 61,304,214 61,825,382 1,919,098 2,310,948 5,842,921

57,905 151,928 170,631 318,383 186,222 181,222 89,735 119,643 193,753

gain gain gain both both gain gain loss gain

BTB-02030131 Hapmap48377-BTA-52225 BTB-01533089 BTA-52234-no-rs Hapmap49357-BTA-87614 ARS-BFGL-BAC-29200 Hapmap40156-BTA103844 BTA-52712-no-rs ARS-BFGL-NGS-98134 ARS-BFGL-NGS-15860 ARS-BFGL-NGS-32701 ARS-BFGL-NGS-62095 BTA-54457-no-rs Hapmap42370-BTA-95032 Hapmap38047-BTA101643 BTA-103933-no-rs Hapmap52611-rs29018692 Hapmap61078-rs29026400 Hapmap33580-BTA136506 ARS-BFGL-NGS-105900 Hapmap30035-BTA155747 ARS-USMARC-ParentEF093510-rs29010035 BTA-54499-no-rs ARS-BFGL-NGS-58344 ARS-BFGL-NGS-94797 BFGL-NGS-113315 ARS-BFGL-NGS-16841 ARS-BFGL-NGS-41433 ARS-BFGL-BAC-31235 ARS-BFGL-NGS-16625 Hapmap31780-BTA147296

BTB-01896293 BTA-52227-no-rs Hapmap48988-BTA-101434 DIAS-275 BTA-86128-no-rs BTB-00207198 BTA-12087-no-rs

4 3 3 4 3 6 3

1 1 1 1 1 4 1

Hapmap41894-BTA-52700 ARS-BFGL-NGS-18270 BTA-20844-no-rs ARS-BFGL-NGS-2644 ARS-BFGL-NGS-23411 ARS-BFGL-NGS-48234 BTA-55233-no-rs ARS-BFGL-NGS-102663

4 3 5 6 5 10 15 3

1 1 2 1 1 1 2 1

BFGL-NGS-116099 BFGL-NGS-113544 BTA-100621-no-rs ARS-BFGL-NGS-29950

5 5 5 3

4 1 2 1

ARS-BFGL-NGS-12323 ARS-BFGL-NGS-43172

3 5

1 1

BTB-00846254

3

1

BTA-54480-no-rs ARS-BFGL-NGS-72105 ARS-BFGL-NGS-16392 ARS-BFGL-NGS-13887 BFGL-NGS-116144 ARS-BFGL-NGS-7101 Hapmap44551-BTA-55507 BFGL-NGS-119695 BFGL-NGS-110066

3 5 5 11 6 5 4 5 3

1 1 1 4 3 1 1 1 3

Unique Unique Unique Unique Unique 0.85% Unique Unique Unique Multiple Unique Unique Unique Multiple Unique 0.85% Unique Multiple Unique Unique Unique Unique Unique Unique Unique 0.85% 0.64% Unique Unique Unique 0.64%

698 699

chr23 chr23

6,844,947 8,790,334

6,932,536 8,866,725

87,590 76,392

gain gain

700 701 702 703 704 705 706 707 708 709 710 711 712 713


9,702,555 15,036,576 22,625,258 24,475,293 26,060,379 27,471,184 30,562,382 32,634,716 34,538,123 35,279,106 36,258,739 48,168,648 48,792,091 50,200,198

9,794,340 15,108,681 22,727,191 24,620,815 26,115,068 27,580,796 30,717,590 32,791,188 34,637,015 35,712,972 36,330,037 48,364,129 49,191,667 50,466,592

91,786 72,106 101,934 145,523 54,690 109,613 155,209 156,473 98,893 433,867 71,299 195,482 399,577 266,395

gain gain gain gain loss loss gain gain loss gain gain gain gain loss

714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730

chr23 chr23 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24 chr24

52,583,723 53,269,261 528,277 3,634,514 4,519,535 5,647,080 6,383,013 7,378,184 8,183,555 17,797,307 22,479,244 28,166,090 28,848,582 29,444,695 29,658,910 43,976,477 45,601,085

52,896,305 53,329,482 1,086,646 3,761,376 4,579,396 5,995,681 6,522,321 7,452,987 8,270,961 17,942,895 22,588,892 28,226,327 28,890,762 29,594,855 29,757,516 44,168,239 45,705,538

312,583 60,222 558,370 126,863 59,862 348,602 139,309 74,804 87,407 145,589 109,649 60,238 42,181 150,161 98,607 191,763 104,454

both gain loss both gain both gain loss gain both gain gain loss gain loss loss gain

ARS-BFGL-NGS-21718 ARS-USMARC-ParentAY929334-no-rs ARS-BFGL-NGS-3147 BFGL-NGS-117744 BTA-55798-no-rs BFGL-NGS-117245 BFGL-NGS-117031 ARS-BFGL-NGS-2116 BTA-56180-no-rs ARS-BFGL-NGS-71037 ARS-BFGL-BAC-46072 UA-IFASA-5340 ARS-BFGL-NGS-59653 BTB-00869068 ARS-BFGL-NGS-38613 Hapmap41132-BTA103312 ARS-BFGL-NGS-17146 ARS-BFGL-NGS-100967 ARS-BFGL-NGS-26076 BTB-00877912 ARS-BFGL-NGS-30774 Hapmap60094-rs29025212 ARS-BFGL-BAC-29242 BTB-00880395 BTA-25359-no-rs ARS-BFGL-BAC-44758 ARS-BFGL-NGS-2686 BTA-112410-no-rs BTA-22620-no-rs BTB-01485872 BTB-01646599 BFGL-NGS-110400 Hapmap51792-BTA103575


4 3

1 1

ARS-BFGL-NGS-3541 ARS-BFGL-NGS-22482 Hapmap44684-BTA-55791 BTA-81631-no-rs Hapmap23601-BTA-155827 ARS-BFGL-NGS-43021 BFGL-NGS-117265 BFGL-NGS-118768 ARS-BFGL-BAC-46073 BFGL-NGS-118652 Hapmap50031-BTA-56452 Hapmap49861-BTA-110754 ARS-BFGL-NGS-89190 ARS-BFGL-NGS-60857

4 3 3 6 4 3 6 5 3 9 3 6 10 10

1 1 4 1 1 1 1 1 1 2 1 1 2 1

BFGL-NGS-118311 Hapmap47467-BTA-100234 BTB-00875143 ARS-BFGL-BAC-42839 ARS-BFGL-NGS-82927 ARS-BFGL-BAC-29834 Hapmap42361-BTA-91303 ARS-BFGL-NGS-37092 BTA-58999-no-rs ARS-BFGL-BAC-44142 ARS-BFGL-NGS-96939 Hapmap29300-BTA-112502 BTB-02012738 BTB-01485274 BTB-00884791 ARS-BFGL-NGS-40737 ARS-BFGL-NGS-67897

11 3 17 5 3 11 4 3 4 4 5 3 3 6 4 5 4

7 1 1 7 1 20 4 1 1 3 3 1 2 3 1 1 1

Unique Unique Unique Unique 0.85% Unique Unique Unique Unique Unique Unique Multiple Unique Unique Multiple Unique 1.48% Unique Unique 1.48% Unique 4.24% 0.85% Unique Unique 0.64% 0.64% Unique Multiple 0.64% Unique Unique Unique

731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760

chr24 chr24 chr24 chr24 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr25 chr26 chr26 chr26 chr26 chr26 chr26

47,424,075 58,552,325 62,513,817 64,694,601 858,957 1,758,319 2,174,283 4,228,928 4,549,534 6,398,912 9,141,839 10,247,990 13,997,023 14,556,628 17,372,122 19,355,496 20,240,718 25,366,865 26,356,047 34,647,264 38,349,639 39,514,818 40,716,235 43,328,713 1,966,809 3,080,985 3,684,275 5,071,319 8,343,595 9,179,169

47,564,395 58,669,661 62,724,316 64,808,820 1,436,322 2,001,673 2,278,557 4,283,716 4,716,785 6,477,087 9,187,283 10,302,525 14,146,973 14,636,884 17,495,434 19,554,955 20,670,441 25,466,424 26,512,299 34,973,007 38,404,852 39,588,051 40,921,050 43,544,545 2,362,507 3,152,913 3,760,091 5,318,046 8,434,010 9,275,307

140,321 117,337 210,500 114,220 577,366 243,355 104,275 54,789 167,252 78,176 45,445 54,536 149,951 80,257 123,313 199,460 429,724 99,560 156,253 325,744 55,214 73,234 204,816 215,833 395,699 71,929 75,817 246,728 90,416 96,139

gain gain loss loss both both gain gain gain gain gain both both both gain gain gain loss loss both gain loss gain gain loss loss loss both loss gain

BTA-58356-no-rs Hapmap43046-BTA-77404 ARS-BFGL-NGS-83715 BTB-01625005 ARS-BFGL-BAC-46926 Hapmap52944-rs29021704 ARS-BFGL-NGS-15055 Hapmap27815-BTC-017722 ARS-BFGL-NGS-78876 Hapmap49602-BTA-41546 BTA-60652-no-rs ARS-BFGL-NGS-17864 ARS-BFGL-BAC-2989 BTA-59544-no-rs Hapmap48012-BTA-59182 ARS-BFGL-NGS-7593 BFGL-NGS-118343 Hapmap43502-BTA-18199 ARS-BFGL-NGS-97895 BFGL-NGS-114938 Hapmap39496-BTA-60118 ARS-BFGL-NGS-83242 ARS-BFGL-NGS-66266 ARS-BFGL-NGS-43920 BTA-26713-no-rs ARS-BFGL-NGS-46925 BTB-00920624 Hapmap60861-rs29018356 BFGL-NGS-109705 BTA-93559-no-rs

761 762 763 764 765


11,816,015 20,994,002 21,323,659 37,094,196 49,049,854

11,901,519 21,068,589 21,444,116 37,171,842 49,133,199

85,505 74,588 120,458 77,647 83,346

gain gain gain loss gain

BTB-00925206 Hapmap44394-BTA-62134 BTB-00930720 ARS-BFGL-NGS-12828 ARS-BFGL-NGS-4369

Hapmap38711-BTA-90355 BTA-58685-no-rs ARS-BFGL-NGS-23259 BTB-01890193 ARS-BFGL-NGS-4009 ARS-BFGL-NGS-104234 ARS-BFGL-NGS-79851 Hapmap22899-BTC-018001 Hapmap25398-BTC-019181 Hapmap32426-BTC-000132 BTA-60642-no-rs BTA-111433-no-rs BTB-01803323 Hapmap32061-BTA-138316 UA-IFASA-5829 BTA-59648-no-rs ARS-BFGL-NGS-95270 BFGL-NGS-113653 UA-IFASA-2352 ARS-BFGL-NGS-38306 ARS-BFGL-NGS-92590 ARS-BFGL-NGS-28673 ARS-BFGL-NGS-25989 BTA-60516-no-rs ARS-BFGL-NGS-41355 BTA-61389-no-rs BTB-00920733 ARS-BFGL-NGS-13248 Hapmap53362-rs29013727 Hapmap35846SCAFFOLD75504_4732 ARS-BFGL-NGS-53115 BTA-60847-no-rs ARS-BFGL-NGS-32238 BTA-05959-rs29020110 ARS-BFGL-NGS-88751

4 5 8 4 17 8 4 3 5 3 3 3 5 3 3 3 7 3 4 10 3 3 8 6 5 3 3 8 4 4

3 2 2 1 3 6 1 2 3 1 1 2 2 6 3 1 2 1 1 3 1 1 1 1 5 1 1 6 1 5

3 4 4 3 4

1 1 1 1 2

0.64% Multiple Multiple Unique 0.64% 1.27% Unique Multiple 0.64% Unique Unique Multiple Multiple 1.27% 0.64% Unique Multiple Unique Unique 0.64% Unique Unique Unique Unique 1.06% Unique Unique 1.27% Unique 1.06% Unique Unique Unique Unique Multiple

766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783

chr26 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr27 chr28 chr28 chr28 chr28

51,049,209 6,017,620 6,187,325 8,130,825 10,744,036 15,717,150 18,669,763 19,900,222 20,029,339 24,427,914 27,169,874 29,760,732 32,972,611 39,529,803 10,430,536 11,127,515 13,862,171 15,191,671

51,572,875 6,089,427 6,398,901 8,211,737 12,042,013 15,813,567 19,011,001 19,982,577 20,180,621 24,527,177 27,285,873 29,830,059 33,169,945 39,614,539 10,563,623 11,460,946 13,916,396 15,243,712

523,667 71,808 211,577 80,913 1,297,978 96,418 341,239 82,356 151,283 99,264 116,000 69,328 197,335 84,737 133,088 333,432 54,226 52,042

both gain both gain both gain both loss gain gain gain gain gain gain gain both gain loss

784 785 786

chr28 chr28 chr28

17,007,778 20,090,604 21,480,908

17,180,327 20,375,994 21,636,401

172,550 285,391 155,494

gain loss gain

787 788 789 790 791 792 793 794 795 796 797 798 799

chr28 chr28 chr28 chr28 chr28 chr28 chr28 chr28 chr29 chr29 chr29 chr29 chr29

23,321,320 24,261,862 24,483,602 26,750,738 33,876,415 35,942,913 36,404,315 39,126,738 4,935,707 11,024,561 11,277,585 14,419,612 19,568,740

23,442,097 24,436,312 24,652,332 26,799,772 33,932,946 36,249,992 36,554,250 39,199,885 5,116,631 11,097,204 11,498,160 14,623,234 19,656,028

120,778 174,451 168,731 49,035 56,532 307,080 149,936 73,148 180,925 72,644 220,576 203,623 87,289

gain loss gain gain both both gain gain gain gain gain loss gain

BFGL-NGS-117200 ARS-BFGL-NGS-14024 BFGL-NGS-116642 BTA-105784-no-rs BTB-02001456 BFGL-NGS-110157 Hapmap43632-BTA-62330 ARS-BFGL-NGS-1612 BTB-01731688 BTB-02036330 BTB-00961421 BTA-62675-no-rs Hapmap49244-BTA-62731 Hapmap47355-BTA-62858 Hapmap55640-rs29014036 Hapmap55826-rs29023262 ARS-BFGL-NGS-108752 Hapmap48649-BTA121210 Hapmap54791-rs29011605 BTA-103766-no-rs Hapmap32810-BTA139892 ARS-BFGL-NGS-46964 Hapmap51909-BTA-63755 BTA-01937-no-rs BFGL-NGS-111868 ARS-BFGL-NGS-99440 BTA-24338-no-rs ARS-BFGL-NGS-74541 Hapmap41045-BTA-64263 ARS-BFGL-NGS-55607 UA-IFASA-7464 ARS-BFGL-NGS-37496 BTB-01008238 BTA-117983-no-rs

BFGL-NGS-114371 ARS-BFGL-NGS-38750 BTA-118887-no-rs BTA-112884-no-rs Hapmap32139-BTA-162043 BTB-00954867 Hapmap38945-BTA-21179 Hapmap46624-BTA-28414 UA-IFASA-1830 Hapmap43310-BTA-62489 ARS-BFGL-NGS-66417 DIAS-320 UA-IFASA-2151 Hapmap57358-rs29014672 Hapmap50192-BTA-104693 Hapmap45049-BTA-64763 BTA-121533-no-rs BFGL-NGS-110719

15 3 5 3 23 4 10 3 5 4 5 3 6 3 5 7 3 3

5 1 7 3 47 1 2 1 1 1 2 1 1 1 1 5 1 1

BTB-00980334 BTB-01171634 BTB-00980953

4 4 6

2 1 2

ARS-BFGL-NGS-15201 Hapmap44554-BTA-63753 BFGL-NGS-114812 ARS-BFGL-NGS-29771 BFGL-NGS-119802 BTA-64181-no-rs ARS-BFGL-NGS-68555 BTA-64266-no-rs BTB-00124185 BTB-01005137 ARS-BFGL-NGS-101192 BTB-01802047 BTA-64987-no-rs

4 5 5 3 3 7 3 3 3 3 6 6 3

2 2 4 1 2 17 1 1 1 1 1 1 1

1.06% Unique 1.48% 0.64% 9.96% Unique Multiple Unique Unique Unique Multiple Unique Unique Unique Unique 1.06% Unique Unique Multiple Unique Multiple Multiple Multiple 0.85% Unique Multiple 3.60% Unique Unique Unique Unique Unique Unique Unique

a

800 801

chr29 chr29

20,005,609 20,438,158

20,095,368 20,560,453

89,760 122,296

gain loss

802 803 804 805 806 807 808


21,133,745 23,407,819 29,072,342 31,707,342 37,461,380 40,596,329 45,391,413

21,369,115 23,628,341 29,246,196 31,837,246 37,527,752 40,748,813 45,488,027

235,371 220,523 173,855 129,905 66,373 152,485 96,615

loss loss gain gain gain gain gain

BTA-64999-no-rs Hapmap22933-BTA140507 BTB-01381621 BTA-05866-rs29020018 BTB-01337464 UA-IFASA-7213 ARS-BFGL-NGS-57118 BTB-01829916 ARS-BFGL-NGS-82048

809 810 811

chr29 chr29 chr29

49,109,423 50,171,073 50,879,371

49,249,117 50,232,014 51,788,033

139,695 60,942 908,663

gain gain both

ARS-BFGL-NGS-86466 BFGL-NGS-118384 ARS-BFGL-NGS-3129


3 3

1 1

Hapmap44267-BTA-65015 UA-IFASA-7930 Hapmap60860-rs29018127 ARS-BFGL-NGS-68193 ARS-BFGL-NGS-106983 ARS-BFGL-NGS-23135 Hapmap36151SCAFFOLD96691_12353 ARS-BFGL-NGS-42102 ARS-BFGL-NGS-61470 ARS-BFGL-NGS-14481

8 6 4 6 3 5 3

1 2 2 1 1 10 2

6 3 25

4 1 14

Unique Unique Unique Multiple Multiple Unique Unique 2.12% Multiple 0.85% Unique 2.97%

The type of the CNV region, was defined as “gain”, “loss”, as well as “both” ( loss and gain events within the same region); b The StartSNP was defined as the start SNP name within this region; c The EndSNP was defined as the end SNP name in this region; d The No. SNP was referred as the number of SNPs accommodated in this region; e The No.Animal was referred as the number of animals representing CNV events in this region; f The Frequency was defined as “Unique” when the CNV region was unique only to one animal, “Multiple” when the CNV region was shared by 2 animals, or shown as the exact proportion of animals having CNV events in this region when the CNV region was shared by at least 3 animals.