nor. CEU. TSI ork ire ser spa tur saa a b. Figure S2: Median-joining network of mtDNA haplotypes based on all variants. Circles represent haplotypes, with area ...
Supplementary Information for: Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions Chiara Batini, Pille Hallast, Åshild J. Vågene, Daniel Zadik, Heidi A. Eriksen, Horolma Pamjav, Antti Sajantila, Jon H. Wetton, Mark A. Jobling Contents: Figure S1: Median-joining network of mtDNA haplotypes based on coding region variants. Figure S2: Median-joining network of mtDNA haplotypes based on all variants. Figure S3: Bayesian skyline plots for the YRI and CHB population samples. Table S1: Sample information. Table S2: Correlations of genetic diversity measures with latitude, longitude and distances from glacial refugia. Table S3: Diversity parameters for the 17 populations for complete mtDNA sequences. Table S4: DNA sequencing information. Table S5: Software tools and parameters used in NGS data analysis. Table S6: Variant validation summary. Table S7: List of possible ‘phantom’ mutations.
1
a haplogroup
3 mutations
H1 H2 H, others HV I J1 J2 K1 K2 T1 T2 U2 U4 U5 U, others V L D,M,N others
b population
3 mutations
pal bas bav den eng fri gre hun nor CEU TSI ork ire ser spa tur saa
Figure S1: Median-joining network of mtDNA haplotypes based on coding region variants. Circles represent haplotypes, with area proportional to frequency, and are coloured according to: a) Haplogroup, as indicated in the key. b) Population, as indicated in the key, with population abbreviations as given in Figure 1. 2
a
haplogroup H1 H2 H_others HV I J1 J2 K1 K2 T1 T2 U2 U4 U5 U_others V L D_M_N others
b
population pal bas bav den eng
fri gre hun nor CEU TSI ork ire ser spa tur saa
Figure S2: Median-joining network of mtDNA haplotypes based on all variants. Circles represent haplotypes, with area proportional to frequency, and are coloured according to: a) Haplogroup, as indicated in the key. b) Population, as indicated in the key, with population abbreviations as given in Figure 1. 3
a
10 6 10 5 10
4
10
3
10 10 10
2 1
YRI
0
0
b
10
20
30
40
50
60
70
80
90
100 110
KYA
10 6 10 5 10
4
10
3
10 10 10
mtDNA
2
MSY
1
CHB
0
0
10
20
30
40
50
60
70
KYA
Figure S3: Bayesian skyline plots for the YRI and CHB population samples. thinner lines show 95% higher posterior density intervals.
4
Table S1: Sample information.
Sample name bas-1 bas-10 bas-11 bas-12 bas-13 bas-14 bas-15 bas-16 bas-17 bas-18 bas-19 bas-2 bas-20 bas-3 bas-4 bas-5 bas-6 bas-7 bas-8 bas-9 bav-12 bav-13 bav-19 bav-26 bav-27 bav-29 bav-30 bav-31 bav-32 bav-38 bav-39 bav-40 bav-41 bav-52 bav-53 bav-54 bav-55 bav-56 bav-57 bav-8 den-104 den-113 den-150 den-152 den-157 den-158 den-176 den-183 den-186 den-189 den-190 den-191 den-192 den-207 den-30 den-34 den-36 den-50-51 den-82-83 den-SN eng-F2 eng-F58 eng-F6 eng-G9 eng-H18 eng-H38
Sequencing Population platform Basque IonTorrent Basque IonTorrent Basque IonTorrent Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina HiSeq Basque IonTorrent Basque Illumina HiSeq Basque Illumina HiSeq Basque Illumina HiSeq Basque Illumina HiSeq Basque IonTorrent Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Basque Illumina MiSeq Bavarian IonTorrent Bavarian Illumina MiSeq Bavarian IonTorrent Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian IonTorrent Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian IonTorrent Bavarian Illumina MiSeq Bavarian Illumina MiSeq Bavarian IonTorrent Danish Illumina MiSeq Danish Illumina MiSeq Danish Illumina HiSeq Danish Illumina MiSeq Danish Illumina HiSeq Danish Illumina HiSeq Danish IonTorrent Danish Illumina HiSeq Danish Illumina HiSeq Danish Illumina HiSeq Danish IonTorrent Danish Illumina HiSeq Danish Illumina HiSeq Danish Illumina HiSeq Danish IonTorrent Danish IonTorrent Danish Illumina MiSeq Danish Illumina MiSeq Danish Illumina MiSeq Danish Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English IonTorrent English Illumina HiSeq English Illumina HiSeq English IonTorrent
Mean coverage (BQ20, MQ50) 72 70 36 2447 2270 2352 15 65 27 25 15 14 55 2252 1738 2830 1623 1660 1613 2333 38 2561 65 1569 1515 3678 2250 2183 76 1957 1914 2208 1911 3027 2766 4334 78 2390 2018 43 3295 2080 20 1827 20 22 102 21 21 20 66 22 23 26 95 57 3354 3075 2287 25 70 58 98 71 42 59
Main filters BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2
5
Sites with missing data 1 7 243 0 0 0 580 3 30 51 170 534 5 0 0 0 0 0 0 0 8 0 5 0 0 0 0 0 11 0 0 0 0 0 0 0 7 0 0 13 0 0 84 0 316 136 7 56 156 300 3 82 33 72 1 4 0 0 0 76 10 8 1 3 46 2
Number of variants compared to rCRS 13 9 10 13 12 34 10 33 30 18 9 13 15 13 34 10 9 10 15 12 12 31 34 14 10 37 2 33 36 36 36 12 28 35 25 33 33 38 38 2 11 12 31 15 32 37 16 15 28 14 13 36 32 13 36 32 34 35 35 14 32 37 35 14 16 15
% missing data 0.000 0.000 0.015 0.000 0.000 0.000 0.035 0.000 0.002 0.003 0.010 0.032 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.005 0.000 0.019 0.008 0.000 0.003 0.009 0.018 0.000 0.005 0.002 0.004 0.000 0.000 0.000 0.000 0.000 0.005 0.001 0.000 0.000 0.000 0.003 0.000
HaploGrep prediction Haplogroup quality (%) H53 87.4 H2a5a1 92.9 H1t1 100 H1 82.7 H3c2a 99 T2b 95.1 H17a 92.1 T2e 99.6 X2c1 100 H4a1a1a1a 100 H1 97.9 V 79.6 V22 100 H1 82.7 K1a4a1e 98.8 H2a5a1a 94.7 H2a5a1a 100 H2a5a1a 94.1 V22 100 H1t1a 97.1 H1a1 100 U7b 94 U4c1a 95 H 79.2 H7 91.7 T2b1 98.3 H2a2a1a 73.2 X2b 93.8 T2b 95.2 K2a5 93.6 T1a1 97.5 HV0 91.8 U4a2 98.6 T1a1 96.4 U5a1a1 100 J1c2q 93.3 J1c2e1 98 W5a1a1 100 U2e1a1 97 H2a2a1 50 H1a 94.2 H3h1 94.6 K1a 91.2 H13a1a1a 96.1 J1c5a1 96.9 T2e1a 92 H11a 89.6 H11a 91.5 U8a1b 94.4 H13a1a1a 93.6 H10e 89.5 K1a4a1 95.4 J1c4 96.4 H1c1 91.2 T1a1k 96.4 J1c4 96.4 K1c1b 96.6 T2 95 T2 95 H1c3b 100 K2a 96.7 U2e1a1 98.7 K1a4a1b 96.8 H1k1 95.8 V2 92 H17c 93.2
eng-N5 eng-O109 eng-O15 eng-O23 eng-O36 eng-O44 eng-O45 eng-O63 eng-O69 eng-O93 eng-W11 eng-W13 eng-W17 eng-W20 CEU-NA06994 CEU-NA07048 CEU-NA07357 CEU-NA10851 CEU-NA11829 CEU-NA11831 CEU-NA11992 CEU-NA11994 CEU-NA12003 CEU-NA12043 CEU-NA12144 CEU-NA12154 CEU-NA12155 CEU-NA12707 CEU-NA12716 CEU-NA12750 CEU-NA12812 CEU-NA12814 CEU-NA12872 CEU-NA12874 fri-1048 fri-1087 fri-1309 fri-1311 fri-1312 fri-1313 fri-1317 fri-1319 fri-1320 fri-1324 fri-1325 fri-1329 fri-1516 fri-1718 fri-1722 fri-1725 fri-1784 fri-1788 fri-1937 fri-1938 gre-1 gre-10 gre-11 gre-12 gre-15 gre-17 gre-2 gre-3 gre-4 gre-5 gre-77 gre-78 gre-79 gre-80 gre-82 gre-83m gre-84m
English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq English IonTorrent English Illumina HiSeq English Illumina HiSeq English Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq French (CEU) Illumina HiSeq Frisian IonTorrent Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian IonTorrent Frisian Illumina HiSeq Frisian Illumina MiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian IonTorrent Frisian Illumina HiSeq Frisian Illumina HiSeq Frisian IonTorrent Greek IonTorrent Greek Illumina HiSeq Greek Illumina MiSeq Greek Illumina HiSeq Greek IonTorrent Greek Illumina HiSeq Greek IonTorrent Greek Illumina HiSeq Greek Illumina HiSeq Greek Illumina HiSeq Greek Illumina MiSeq Greek IonTorrent Greek Illumina HiSeq Greek Illumina HiSeq Greek Illumina HiSeq Greek Illumina MiSeq Greek Illumina MiSeq
162 86 75 133 167 80 128 68 102 72 75 86 58 51 83 94 95 108 100 81 102 132 84 82 81 95 71 109 206 83 109 83 72 75 73 27 44 53 42 3568 20 17 23 23 24 30 19 22 25 23 78 33 18 57 103 19 2702 13 73 19 43 17 20 21 3503 78 18 19 15 3159 3689
BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2
6
2 2 3 0 0 5 3 3 2 1 3 3 4 2 2 1 4 1 3 3 0 0 2 4 5 1 4 2 0 12 2 2 3 4 3 66 25 1 28 0 256 210 60 76 16 49 11 207 4 193 1 10 249 6 2 111 0 350 6 270 53 188 282 133 0 2 330 207 410 0 0
29 10 14 17 13 11 35 30 10 35 29 4 10 15 27 6 30 16 39 9 28 35 34 34 13 30 20 11 14 39 12 29 11 28 11 14 31 10 11 28 24 13 17 14 28 33 35 13 13 33 17 8 33 30 33 12 34 27 45 31 13 16 35 34 38 26 10 18 13 15 35
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.004 0.002 0.000 0.002 0.000 0.015 0.013 0.004 0.005 0.001 0.003 0.001 0.012 0.000 0.012 0.000 0.001 0.015 0.000 0.000 0.007 0.000 0.021 0.000 0.016 0.003 0.011 0.017 0.008 0.000 0.000 0.020 0.012 0.025 0.000 0.000
J1c1b H H1a5 V H1o H7 T1a1 J1c3a1 H5a1 I2 J1c3a1 H2a2a1 H24b H1b1 U5b2a1a1 H2a1 U5a1c2a V16 T2a1a H5'36 U5a2d1a T2b4b T2b1 T1 H1e1a J1c5a1 H8c H1b1 H1ae2a T2f1a1 H1 U5a1b1a2 HV6 J1c8a H17 H1a1 X2c1 H H1c2a J1c5 U5a1a1 H11a V3c H1a3a U5a1a1 K1a4a1b I3a H11a H31 J1c7a H5a6 H T1a U5a2c3a T1a1l H7c4 K1a12a1a J1c M1a1 X1 H9a H8a K1a T1a1l N1b1a4 U6a1a1 H1 HV1b V V6 J1c7a
96.6 92.6 99.5 94.3 92.5 98 96.8 95.4 100 95.7 98.5 50 95.4 88.7 100 100 92.9 96.8 94 91.5 100 97.2 98.3 96.4 93.7 100 86 96.5 91.4 88.6 94.3 98.7 100 98.4 93.5 96.5 94.3 86.8 100 96 93.6 98.2 98.4 96.8 96.5 99.4 96.7 98.2 98.5 96.9 89.7 98.6 96.3 93.2 100 91.7 96.8 95.8 94.7 91.6 95.7 96.5 90.1 98.2 96.6 100 95.7 86.6 87.6 96.6 96.4
gre-85m gre-86 gre-87 hun-1 hun-2 hun-25 hun-26 hun-27 hun-28 hun-29 hun-3 hun-33 hun-34 hun-35 hun-37 hun-38 hun-39 hun-40 hun-43 hun-46 hun-47 hun-5 hun-9 ire-0052 ire-0053 ire-0059 ire-0068 ire-0078 ire-0093 ire-0095 ire-0100 ire-0107 ire-0109 ire-0114 ire-0116 ire-0120 ire-0130 ire-0136 ire-112 ire-132 ire-55 ire-74 ire-94 TSI-NA20510 TSI-NA20538 TSI-NA20543 TSI-NA20581 TSI-NA20586 TSI-NA20588 TSI-NA20752 TSI-NA20758 TSI-NA20759 TSI-NA20765 TSI-NA20783 TSI-NA20785 TSI-NA20792 TSI-NA20796 TSI-NA20798 TSI-NA20803 TSI-NA20805 TSI-NA20806 TSI-NA20810 TSI-NA20815 nor-13 nor-14 nor-15 nor-16 nor-17 nor-18 nor-2 nor-20
Greek Greek Greek Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Hungarian Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Irish Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Italian (TSI) Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian
Illumina MiSeq Illumina MiSeq IonTorrent IonTorrent Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq Illumina HiSeq Illumina MiSeq Illumina HiSeq IonTorrent Illumina MiSeq Illumina HiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq IonTorrent Illumina HiSeq IonTorrent Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina HiSeq Illumina HiSeq IonTorrent IonTorrent Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq IonTorrent
3164 2204 57 76 2305 40 2647 2342 3914 77 2971 2148 3659 29 14 3419 24 81 4530 22 1983 57 3464 2035 39 23 67 3040 2406 63 3774 20 23 73 84 19 3567 3455 14 17 1821 1622 22 87 100 72 79 65 78 55 141 65 91 146 124 83 59 71 60 43 54 64 49 104 27 35 36 3239 2712 2216 71
BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2
7
0 0 3 4 0 139 0 0 0 3 0 0 0 482 190 0 221 1 0 205 0 2 0 0 106 305 7 0 0 1 0 442 109 0 1 438 0 0 608 441 0 0 209 1 4 2 6 2 3 6 0 1 1 3 1 1 7 3 5 2 3 0 1 0 160 84 27 0 0 0 1
34 32 26 34 36 12 40 2 36 30 32 9 11 31 32 10 15 34 10 11 11 32 8 16 17 37 32 30 38 11 9 11 31 14 11 30 13 31 37 40 33 28 40 33 10 16 38 11 11 35 39 40 28 36 31 13 12 12 13 27 18 17 10 14 37 34 9 27 37 14 13
0.000 0.000 0.000 0.000 0.000 0.008 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.029 0.011 0.000 0.013 0.000 0.000 0.012 0.000 0.000 0.000 0.000 0.006 0.018 0.000 0.000 0.000 0.000 0.000 0.027 0.007 0.000 0.000 0.026 0.000 0.000 0.037 0.027 0.000 0.000 0.013 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.010 0.005 0.002 0.000 0.000 0.000 0.000
T1b3 T2 U5a1a1 T2b5 U4c1a H1c20 J2a1a1a3 H2a2a1 K2b1b U8b1b U6a5 H24a HV T2b I4a1 H1 H11a2a T1b4 H20 H1 H1 K2a10 H10b H6a1b4 V1a T2b3b J1c3e1 J1c1b2 I1a1 H56a1 H3 H16 K2a10 H1m1 H1c1 K1a12 H3a1 K2a6 K1c1 U2e3a T1a1 X2b+226 U2e3a W6 H82 H1au T1a2a H1ba H23 J2a2b2 T2c1d K1a1b2a1a U5a2b2 T2c1a2 J1c3e2 H1b1 H7 H15b1 H1e2d U5a1g H13b1b H1e H44a V T2a1a K1a3 H2a1 U5a1a1 D2 H13a1a1a H6a1a
98.8 93.9 98.2 99.3 97.9 93.4 98.3 50 99.6 92.1 90 100 94.6 100 95.4 94.3 90.1 91.9 89.9 89.6 92.7 98.7 100 95.7 96.8 98.1 97.5 99.1 98.1 100 93.4 97.9 100 97 100 97.7 96.2 100 92.8 95 100 100 94.5 96.6 89.8 81.5 100 92.2 91.8 100 97.1 97.1 99.8 95.5 98.1 95.3 85.4 100 93.5 92.9 93.5 81.7 100 100 96.4 96.1 87.1 99.3 95.4 99.6 100
nor-21 nor-23 nor-24 nor-25 nor-26 nor-27 nor-28 nor-29 nor-3 nor-7 nor-8 nor-9 ork-004 ork-007 ork-008 ork-010 ork-022m ork-026m ork-036m ork-525 ork-552 ork-564 ork-565 ork-567 ork-571 ork-573 ork-575 ork-577 ork-579 ork-583 ork-584 ork-585 pal-4918 pal-4919 pal-4921 pal-4922 pal-4929 pal-4940 pal-4941 pal-4942 pal-4943 pal-4947 pal-5047 pal-5048 pal-5225 pal-5232 pal-5257 pal-5341 pal-5365 pal-5366 pal-5370 pal-5420 saa-1 saa-10 saa-11 saa-12 saa-13 saa-14 saa-15 saa-16 saa-17 saa-18 saa-19 saa-2 saa-20 saa-3 saa-4 saa-5 saa-6 saa-7 saa-8
Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Norwegian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Orcadian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Palestinian Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami Saami
Illumina MiSeq Illumina HiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina MiSeq Illumina MiSeq IonTorrent IonTorrent IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina MiSeq IonTorrent IonTorrent IonTorrent Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq Illumina MiSeq Illumina HiSeq IonTorrent IonTorrent Illumina MiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq
3215 28 36 1654 2890 1508 21 65 34 3213 2206 62 68 65 103 119 72 77 94 58 109 157 66 91 53 47 131 59 64 58 70 53 65 134 75 82 107 102 101 123 119 155 89 91 109 96 97 97 167 102 70 73 2381 80 43 101 25 2860 2010 2604 2544 21 1972 19 73 77 3111 33 1927 2687 2048
BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2
8
0 152 77 0 0 0 126 1 45 0 0 1 7 2 1 1 2 2 1 4 6 0 2 2 24 5 1 5 4 28 1 1 3 1 3 2 3 0 4 1 2 3 2 1 3 1 1 3 1 1 2 7 0 2 4 12 209 0 0 0 0 532 1 348 1 14 0 106 0 0 0
32 38 33 28 27 6 33 28 38 33 13 39 28 11 37 31 8 10 34 31 33 29 28 39 12 29 11 37 31 31 31 30 37 30 34 28 15 35 37 54 9 18 27 14 35 39 38 10 32 27 36 41 30 26 17 40 30 27 12 30 12 29 29 28 31 17 30 28 29 29 30
0.000 0.009 0.005 0.000 0.000 0.000 0.008 0.000 0.003 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.002 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.013 0.000 0.000 0.000 0.000 0.032 0.000 0.021 0.000 0.001 0.000 0.006 0.000 0.000 0.000
K1c1b K2a11 T2b2b U5a1b1e U5b1b2 H2a5 K1c2 U5a1b1e T2a1b1a1 T2b2b V3c T2b25 U5b2b2 H5b2 J1c2l X2b8 H23 H66a I2 J1c2e1 T1a1 X2b U4a2 J1b1a1a H16a1 J1c3g H5b2 T2b23a U5b2c2b X2b8 U5b2c2b J1c3b1a T2b U6a3d1a L3e3a M30 HV1a'b'c I U1a1b L2a1 H HV1 U5a1a1 HV0c J1b1a1 T2a1b1a1b K1b1c H1 L3e1 U5a2a1 U1a1 N1b1a U5b1b1a U5b1b1a V7a1 D5a3a1a U5b1b1a U5b1b1a V U5b1b1a V U5b1b1a U5b1b1a U5b1b1a U5b1b1a V7a1 U5b1b1a U5b1b1a U5b1b1a U5b1b1a U5b1b1a
98.4 91.6 95.9 97.4 97.1 100 98.4 97.4 98 95.9 96.5 95.7 100 100 95.7 98.1 100 93.4 96.7 96.1 95.9 96.8 98.5 98.1 97 96.8 100 98.7 98.2 98.1 98.2 98.8 90.3 98.5 97.8 96.6 95 89.8 95 95 92.6 83.3 98.2 92.6 99.6 93.3 97.6 93.2 94.8 98.1 96.2 95.4 96.4 97.7 100 99.4 95.4 100 100 95.4 100 92.8 96.8 91 94.5 100 95.4 97.6 98 96.8 96.8
saa-9 ser-1 ser-12 ser-13 ser-16 ser-19 ser-2 ser-20 ser-21 ser-23 ser-24 ser-26 ser-27 ser-28 ser-3 ser-30 ser-4 ser-5 ser-6 ser-7 ser-9 spa-14 spa-15 spa-2 spa-20 spa-22 spa-25 spa-26u spa-31 spa-32 spa-37 spa-40 spa-41 spa-47 spa-51 spa-53 spa-54u spa-60 spa-60u spa-62 spa-63 tur-1 tur-10 tur-11 tur-12 tur-13 tur-14 tur-15 tur-16 tur-17 tur-18 tur-19 tur-2 tur-21 tur-3 tur-4 tur-5 tur-6 tur-7 tur-8 tur-9
Saami Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Serbian Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Spanish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish Turkish
Illumina MiSeq IonTorrent IonTorrent IonTorrent Illumina MiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq IonTorrent Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina HiSeq IonTorrent Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq IonTorrent IonTorrent IonTorrent Illumina HiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina HiSeq Illumina MiSeq Illumina MiSeq IonTorrent Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq Illumina MiSeq
2521 70 87 57 1734 12 11 24 54 24 21 15 2591 1846 2097 74 1850 1709 2120 2152 2771 151 2025 1916 1831 2067 1681 19 86 1065 2150 3299 19 58 2385 2000 33 1888 68 2009 2201 35 87 62 15 20 2318 1763 65 2076 22 3092 1891 66 1590 2486 2572 1703 2727 2258 2285
BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP1 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2 BQ20, MQ50, DP2
0 10 2 3 0 310 178 54 8 148 837 559 0 0 0 5 0 0 0 0 0 1 0 0 0 0 0 291 1 0 0 0 302 1 0 0 111 0 6 0 0 420 13 7 255 343 0 0 2 0 198 0 0 6 3 0 1 0 0 0 0
17 28 36 34 15 11 36 37 11 28 9 35 12 33 10 30 33 14 33 29 13 30 10 29 13 39 11 13 31 33 57 11 31 15 16 15 12 32 34 7 11 24 29 15 34 34 41 34 24 29 26 34 9 35 18 37 46 10 33 34 25
0.000 0.001 0.000 0.000 0.000 0.019 0.011 0.003 0.000 0.009 0.051 0.034 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.018 0.000 0.000 0.000 0.000 0.018 0.000 0.000 0.000 0.007 0.000 0.000 0.000 0.000 0.025 0.001 0.000 0.015 0.021 0.000 0.000 0.000 0.000 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
V7a1 U4a T2a1a1 U4b1a1a1 H6a1a H12 I1a1 T2b H83 U4a H T1a1l H5n U2d H7g J2b1c T2b2b1 H1u T2b4a U4a2a H13a1a1e J1b2 H1 U5a1i H1c K1a H3 H1c4a K2a J1c3 L2a1 H1e1a U5a1a1 HV0f H13a2c H8c V J1c2e2 K1a1b1 H3 H1c4 X2f A H13a2b2 U2d2 T2a1b I1c1a T2b13a HV2a U4a2b U5a1a1 J1b3b H N1a3 HV4 T2b C4a1d H5 J1d3b U1b R0a2
100 98 96 98.5 100 96.9 95 93.8 88.2 93 91.4 97.6 93.1 94.2 94.8 100 98.3 86.4 98.2 95 100 96.7 95.9 98.1 92.1 87.7 93.5 95.3 100 97.8 94.2 100 90.8 88.7 92.4 99 100 98.8 93.2 100 95 98.4 90.6 87.8 91.4 94.2 96.3 100 84.9 98.1 94 96.3 87.8 91.6 83.6 93.5 95.4 94.3 96 94.1 88.8
CHB-NA18558 CHB-NA18561 CHB-NA18562 CHB-NA18572 CHB-NA18603 CHB-NA18605 CHB-NA18608 CHB-NA18609 CHB-NA18611
CHB CHB CHB CHB CHB CHB CHB CHB CHB
Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq
64 88 76 65 74 106 97 54 66
BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1
3 5 4 4 4 1 1 4 6
38 29 31 28 30 44 40 37 31
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
D5a2a2 F1d D4i A17 F1d1 D5c1 M11c F2c2 A5b1
98.3 90 98.3 99.1 96.5 94.7 92.7 95.4 92.8
9
CHB-NA18612 CHB-NA18620 CHB-NA18621 CHB-NA18622
CHB CHB CHB CHB
Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq
46 49 59 64
BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1
24 5 7 5
28 33 30 39
0.001 0.000 0.000 0.000
CHB-NA18623 CHB-NA18624 CHB-NA18632 CHB-NA18633 CHB-NA18635 CHB-NA18636 CHB-NA18637 YRI-NA18501 YRI-NA18504 YRI-NA18507 YRI-NA18516 YRI-NA18522 YRI-NA18853 YRI-NA18856 YRI-NA18871 YRI-NA19098 YRI-NA19119 YRI-NA19130 YRI-NA19138 YRI-NA19144 YRI-NA19153 YRI-NA19160 YRI-NA19171 YRI-NA19200 YRI-NA19203 YRI-NA19207 YRI-NA19223
CHB CHB CHB CHB CHB CHB CHB YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI YRI
Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq
59 63 66 65 79 80 92 79 109 81 88 97 101 62 73 116 60 60 67 63 96 65 65 81 102 56 61
BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1 BQ20, MQ50, DP1
3 3 4 3 1 3 7 22 0 22 0 3 5 5 22 1 4 2 10 4 1 4 8 1 1 16 10
40 28 28 33 40 41 36 76 33 77 69 72 32 56 39 36 40 58 33 37 38 39 39 36 77 75 76
0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000 0.001 0.000 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001
N9a9 F1a1c A19 Z3 D5a2a1+@ 16172 F2b1 A15 D4k G2a1f M7b1a1a G2b1a2 L1b1a18 L3e2b L1b1a3 L2b1a3 L2b1a3 L3e2b L2a1b3 L3b1a1 L3b1a L3b1a7a L2a1c3b2 L3e2b3 L3d5a L3d2b L3e2b2 L3e3b L3e3b L1b1a7 L1b1a3 L1b1a3
90 93.3 95.2 96.9 96 93.7 92.9 96.4 97.2 97 97.4 98.6 95.2 100 99.4 98 95.7 97.4 92.9 91.6 94.4 96 94.7 96.4 92.1 92.3 98.5 100 100 99.3 100
BQ: base quality; MQ: mapping quality; DP: depth; rCRS: revised Cambridge reference sequence. YRI: Yoruba in Ibadan, Nigeria; CHB: Han Chinese in Beijing, China; CEU: Utah Residents with Northern and Western European ancestry; TSI: Toscani in Italy.
10
Table S2: Correlations of genetic diversity measures with latitude, longitude and distances from glacial refugia.
Pearson
-0.748 (0.001)
0.43 (0.085)
km from FrancoCantabrian refugium (p) 0.378 (0.134)
Spearman
-0.675 (0.003)
0.456 (0.066)
0.362 (0.153)
-0.587 (0.013)
Pearson
-0.566 (0.018)
0.407 (0.105)
0.424 (0.09)
-0.575 (0.016)
Spearman
-0.491 (0.045)
0.477 (0.053)
0.522 (0.031)
-0.5 (0.041)
All 17 populations S/usable loci nd
latitude (p)
all except saami, palestinian, turkish S/usable loci nd
latitude (p) Pearson
longitude (p)
longitude (p)
km from NearEast refugium (p) -0.68 (0.003)
km from FrancoCantabrian refugium (p)
km from NearEast refugium (p)
-0.32 (0.264)
0.507 (0.064)
0.455 (0.102)
-0.474 (0.087)
Spearman
-0.416 (0.139)
0.49 (0.075)
0.383 (0.176)
-0.405 (0.151)
Pearson
0.024 (0.935)
0.52 (0.057)
0.697 (0.006)
-0.305 (0.289)
Spearman
-0.068 (0.817)
0.531 (0.051)
0.678 (0.008)
-0.253 (0.383)
S: number of polymorphic sites; nd: nucleotide diversity; p: p-value - blue color highlights significant (
