Y-SNP calls for Chachapoyas

Below are the Y-SNP calls for the seven Chachapoyas. Positive calls are in bold, and negative calls are in non-bold.

DNA evidence indicates that NA40 was female, and that NA41, NA43, NA47, and NA50 were possibly female, but I’m including the Y-SNP calls for all of the samples because the DNA-based sex determination for low-coverage genomes like these is not always correct.

NA39

C1a1a1-Z7985
C1b1-K246
C1b1a1a-Z12508
C1b1a1a1-Z12520
D1b2-Z14798
E-M5531
E1a-Z15429
E1a2-Z15143
E1a2-Z15150
E1a2a2-Z15207
E1a2b-Z15089
E1a2b1a1a1-Z14912
E1b1a1a1c2c3a2-Z16106
E2b-Z15799
E2b-Z15833
E2b-Z15872
G-Z6318
G2-M3273/PF2895
G2a1a1-Z8013
G2a2b2a1c1a1-Z6044
G2a2b2b1a-PF3394
H1a1d1-Z14607
H1a1d1-Z14656
H1a1d2c1a1-Z12541
H1a2a1-Z14772
H1b1-Z14111
H1b2-Z14274
H1b2a-Z14388
H3-Z13573
H3a2b-Z12869
H3b-Z13923
H3b1-Z13710
H3b1-Z13800
O2-L463
O3a1c-002611/IMS-JST002611
Q1b-Y1137.2/Z1543.2
Q1b1-FGC1777/Y2020
Q1b1a-FGC1811/Y2124

NA40

A1a-V58
C1b1-K246
C1b1a-Z12491
C1b1a1a1-Z12520
D1b1d1a-Z14833
E-M5531
E-PF1618
E1a2a1b1a-Z15357
E1b1a1a1c2a1-Z15992
E2-CTS1430
E2b-CTS3677
E2b-Z15833
G-CTS11670
G-M3605/PF3077
G-Z3247
G-Z3285
G2-CTS4703/M3533/PF2976
G2-M3273/PF2895
G2-Z6474
G2a2a1b1-Z6490
G2b-Z8018
H1a1d2c1a1-Z12542
H1a2a1-Z14732
H1b2-Z14274
H3a-Z13441
H3a-Z16822
H3a2a-Z12734
H3a2b-Z12869
H3b1-Z13710
H3b1-Z13800
Q1b2-Y1154

NA41

E1a-Z15508
E1b1a1a1-L86.1
E2b-Z15823
E2b-Z15833
E2b-Z15852
G-Z6318
G2-Z6474
H1b2-Z14274
H1b2a-Z14401
H3-Z13526
H3a2-Z12773
H3b1-Z13710

NA42

C1a1a2-Z7232
C1b1a-Z12491
C1b2-Z12352
C2e2-Z12260
D1b1d1-Z14876
D1b2-Z14798
D1b2a-CTS11619
E-CTS939/M5389
E-P169/Page54/PF1878
E-Z15668
E1a-CTS340
E1a-Z15485
E1a2-CTS3256
E1a2-Z15154
E1a2a2-Z15241
E1a2b1a1a1-Z14925
E1a2b1a2-Z14984
E1b1-P2/PF1940/PN2
E1b1a1a1c2c1a-Z16078
E1b1a1a1c2c1a-Z16102
E1b1a1a1c2c3b1-Z16138
E1b1a1a1c2c3b1-Z16151
E1b1a1a1c2c3b1-Z16156
E1b1b1b2b1-P72
E1b2-P75
E2-CTS2838
E2-P68
E2b-CTS3677
E2b-CTS6931
E2b-CTS9568
E2b-CTS9847
E2b-Z15799
E2b-Z15823
E2b-Z15833
E2b-Z15847
G-Z3247
G-Z3285
G-Z3507
G-Z6318
G2-Z6474
G2a2a1b1-CTS3850/Z2051
G2a2b2a1-Z3245
G2a2b2a1-Z6294
G2a2b2b-PF3375
H1a1d2-Z14515
H1a1d2b2a-Z14473
H1a2a-Z4422
H1a2a1-Z14732
H1a2a1-Z14761
H1a2a1-Z14772
H1b1-Z14065
H1b1-Z14111
H1b2-Z14274
H1b2-Z14307
H1b2a-Z14374
H1b2a-Z14375
H1b2a-Z14386
H3-Z13527
H3a-Z13438
H3a1-Z13133
H3a2-Z12763
H3a2a-Z12734
H3a2a2-Z12697
H3a2b-Z12869
H3b1-Z13694
H3b1-Z13710
H3b1-Z13793
H3b1-Z13800
N1c2b-P43
P-P69
Q1b-Y1071
Q1b-Y1098
Q1b-Y1109
Q1b1-FGC1861/Y2084
R1-P238/PF6115

NA43

B2b2-P112
E1a2-Z15154
E1b1a1a1c2-Z15936
H1b2-Z14274
H1b2a-Z14374
H1b2a-Z14375
H3a2-Z12773
H3a2a-Z12734
H3a2b-Z12871
H3b-Z13886
H3b1-Z13710

NA47

C1b1a1a1-Z12520
D1b2-Z14798
E1a2-Z15118
E1b1a1a1c2c3b1-Z16156
E1b1b1a-V68
G-Z3247
G-Z6318
H1a2a1-Z14772
H1b2-Z14274
H1b2-Z14307

NA50

D1b2-Z14798
E1a2a2-Z15208
H1a1d1-Z14586
H1a2a1-Z14772
H1b2-Z14274
H3a2-Z12786

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