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Thread: Population genomics of the Viking world (bioxiv, 2019, Copenhagen)

  1. #781
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    Kyrgyzstan
    Quote Originally Posted by Wing Genealogist View Post
    The raw data is out at: https://www.ebi.ac.uk/ena/browser/te...ery=PRJEB37976 But how do you go from the VK### used in the paper to find the sample which are named ERX4058###?
    Ok, there is a way to do it. Go to :https://www.ebi.ac.uk/ena/browser/view/PRJEB37976 and find "Download report" as "TSV". Click on TSV. You will get a long text file, which looks like this:

    study_accession sample_accession experiment_accession run_accession tax_id scientific_name fastq_ftp submitted_ftp sra_ftp
    PRJEB37976 SAMEA6799838 ERX4058262 ERR4059477 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/007/ERR4059477/ERR4059477.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059477/VK1.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/007/ERR4059477
    PRJEB37976 SAMEA6799839 ERX4058263 ERR4059478 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/008/ERR4059478/ERR4059478.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059478/VK6.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/008/ERR4059478
    PRJEB37976 SAMEA6799840 ERX4058264 ERR4059479 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/009/ERR4059479/ERR4059479.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059479/VK9.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/009/ERR4059479
    PRJEB37976 SAMEA6799841 ERX4058265 ERR4059480 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/000/ERR4059480/ERR4059480.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059480/VK11.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/000/ERR4059480
    PRJEB37976 SAMEA6799842 ERX4058266 ERR4059481 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/001/ERR4059481/ERR4059481.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059481/VK14.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/001/ERR4059481
    PRJEB37976 SAMEA6799843 ERX4058267 ERR4059482 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/002/ERR4059482/ERR4059482.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059482/VK15.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/002/ERR4059482

    and so on.

    So if you look at the last line here, it says:

    PRJEB37976 SAMEA6799843 ERX4058267 ERR4059482 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/002/ERR4059482/ERR4059482.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059482/VK15.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/002/ERR4059482

    So VK15 corresponds to ERX4058267

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     Onur Dincer (09-17-2020),  perttimp (09-17-2020),  Wing Genealogist (09-17-2020)

  3. #782
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    Y-DNA (P)
    E-Y140446
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    H4a1a4b2
    Y-DNA (M)
    I-Z60
    mtDNA (P)
    V7a

    Took some time today to call downstream SNPs for VK474, identified as Gotland.SG_VA and L791+ in the paper. E-L791 is mostly found in the Near East so its presence here is quite interesting, especially with this individual having over 95% Balto-Slavic-like ancestry. VK474's BAM file was 4.9 GBs. 49/126 (39%) of checked SNPs were no-calls.

    I checked for 126 SNPs at or downstream E-L791 using the Integrative Genomics Viewer (IGV). His path is almost certainly E-L791 > Y4971 > BY36952. BY36952 is the name of an relatively young Iraqi/Kuwaiti clade on FTDNA, whose name is E-Y39447 on YFull. There are 32 SNPs at the E-Y39447 level on YFull. VK474 was only positive for BY36952, but was negative for 21, and the other 10 were no-calls. I interpret this as VK474 belonging to an ancient (and likely extinct) split off from this clade, probably to the order of 5000 years ago.

    Now, it should be said that BY36952 is found in both Haplogroup E and Haplogroup O, and perhaps this call is inaccurate. BY36952 had two positive reads so I believe it is an accurate call. While I checked all publicly available SNPs downstream E-L791, both Y4972 and Y4976 were no-calls. As there are at least three basal lines of E-Y4972 (3 on FTDNA and 2 on YFull), if the above positive call is questionable he could in fact be somewhere downstream E-Y4972 (but still outside the known subclades downstream). I would love a more experienced member's opinion on the issue.

    Looking forward to more interesting results! Let me know if you have any questions.

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  5. #783
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    Y-DNA (P)
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    J2a1 Z6065>Y7708>M47
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    H1j

    United States of America Lebanon Germany United Kingdom Belgium Switzerland
    Quote Originally Posted by Dewsloth View Post
    and VK333 is just holding at "DF19" unless someone finds something else in there...
    If someone could check VK333, please, or tell me what I need to do/learn/download to check him myself.
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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     MitchellSince1893 (09-17-2020)

  7. #784
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    T2B-T152C

    Canada England Scotland Germany Poland France
    I'm assuming a lot of people will be very excited to see how VK201, VK202, VK203, and VK207 will plot as these are potentially Orcadian Picts?
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Scottish 17.96%, Scotch-Irish 12.5%, Eastern German 12.5%, Eastern European (Likely Polish possibly including Romanian) 12.5%, French 7.81%, Native American (Saulteaux and Assiniboine) 2.34%, and Colonial American, 3.125%, which cannot be traced with certainty. With certainty, there is Dutch (at least 1.36%) and some English.

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  9. #785
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    Y-DNA (P)
    U152>L2>Z49>Z142>
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    I2a2a1b2a1b1>Y4925
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    Quote Originally Posted by MitchellSince1893 View Post
    Im really interested in samples VK40 and VK138 as they are currently the oldest known samples on my y dna branch R-U152>L2>Z49>Z142. One is confirmed to be Z142>Z12222 , but there should be quite a few SNPs below this level.
    They are

    PRJEB37976 SAMEA6799862 ERX4058286 ERR4059501 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/001/ERR4059501/ERR4059501.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059501/VK40.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/001/ERR4059501

    PRJEB37976 SAMEA6799915 ERX4058339 ERR4059554 9606 Homo sapiens ftp.sra.ebi.ac.uk/vol1/fastq/ERR405/004/ERR4059554/ERR4059554.fastq.gz ftp.sra.ebi.ac.uk/vol1/run/ERR405/ERR4059554/VK138.final.bam ftp.sra.ebi.ac.uk/vol1/err/ERR405/004/ERR4059554


    I would be grateful if some one could look at these 2. Looking to see if they are positive for any of these SNPs

    FGC12378/79/80/81/82/83, FGC47869, FGC12401/02/03/04/05, FGC47900, Y9080

    Or any of these
    http://www.ytree.net/BlockInfo.php?blockID=1806
    Last edited by MitchellSince1893; 09-17-2020 at 01:40 AM.
    37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 3% Ireland, 3% Nordic, 2% French/Dutch, 1% India
    Hidden Content

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     Onur Dincer (09-17-2020)

  11. #786
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    I know this may seem like a silly question, but does "read count" on ENA indicate sample coverage?

     
    read_count sample_alias
    668392859 VK1
    377914192 VK42
    356596347 VK70
    351122596 VK190
    342730508 VK522
    320900209 VK50
    247578826 VK102
    242836826 VK58
    232851793 VK118
    225580173 VK475
    220439470 VK547
    217676732 VK521
    216744468 VK533
    212503009 VK532
    207409901 VK166
    196413078 VK46
    187371101 VK129
    184885004 VK29
    174155909 VK98
    164756976 VK548
    159793762 VK6
    144096997 VK468
    141157285 VK154
    139199426 VK429
    130776844 VK87
    129553519 VK541
    120586523 VK176
    120485518 VK230
    120249957 VK513
    117862966 VK433
    116240313 VK551
    114311116 VK448
    111880296 VK279
    109547576 VK303
    102032525 VK443
    97895696 VK496
    97719255 VK281
    97691257 VK487
    97129169 VK40
    96776328 VK337
    96064745 VK179
    95803182 VK160
    94301012 VK483
    93742165 VK526
    92658708 VK512
    92338156 VK486
    91428403 VK95
    90120575 VK550
    89133081 VK221
    89085104 VK493
    86113291 VK101
    85887036 VK520
    85808064 VK110
    85778561 VK25
    84969325 VK549
    84934413 VK220
    84738508 VK420
    84540333 VK332
    84145797 VK479
    83807114 VK511
    83747029 VK545
    82913540 VK489
    81733089 VK529
    81721155 VK399
    81638942 VK508
    80921424 VK446
    80733728 VK474
    80207571 VK237
    79150025 VK274
    78881624 VK478
    77653165 VK141
    77584738 VK385
    77454619 VK402
    77152272 VK357
    76368114 VK510
    75958645 VK497
    75925983 VK544
    74729780 VK539
    74489569 VK524
    73617249 VK342
    73206173 VK350
    73060738 VK184
    72747411 VK324
    72461604 VK219
    72072870 VK481
    71909103 VK390
    71836125 VK491
    71727684 VK403
    71654762 VK455
    71624918 VK552
    71604296 VK364
    71560150 VK449
    70657077 VK528
    70578548 VK414
    69760463 VK316
    69560519 VK404
    69530103 VK537
    69386355 VK308
    69297034 VK445
    69167766 VK323
    69035231 VK473
    68591239 VK322
    68152810 VK346
    68061948 VK397
    67598053 VK442
    67494270 VK395
    67412274 VK509
    67228579 VK417
    67180771 VK553
    67146790 VK329
    66897204 VK415
    66750978 VK419
    66596996 VK238
    66416824 VK263
    66358637 VK516
    66087935 VK542
    65848325 VK505
    65845023 VK128
    65543896 VK349
    65365148 VK531
    65135729 VK353
    64782532 VK406
    64539523 VK456
    64469403 VK273
    64446042 VK256
    64270937 VK236
    64231148 VK326
    64187032 VK398
    64084565 VK328
    63991307 VK333
    63986586 VK84
    63960111 VK343
    63911633 VK372
    63333914 VK290
    63157381 VK396
    63024926 VK336
    62912501 VK202
    62620871 VK320
    62576753 VK535
    62377270 VK265
    62115797 VK173
    62104506 VK389
    62002854 VK538
    61841723 VK484
    61701518 VK201
    61256263 VK363
    61228329 VK327
    61174873 VK122
    61153952 VK506
    61129634 VK370
    60880467 VK495
    60263750 VK146
    60116285 VK34
    59698860 VK401
    59670561 VK555
    59662437 VK361
    59347987 VK534
    59330761 VK514
    59132681 VK203
    58824844 VK422
    58745549 VK384
    58699422 VK498
    58501441 VK168
    58435226 VK262
    58301850 VK387
    58026675 VK355
    57233845 VK99
    57225050 VK317
    57143308 VK294
    57079919 VK345
    57058815 VK418
    56937839 VK393
    56711969 VK368
    56632696 VK172
    56257843 VK352
    56156304 VK523
    56051103 VK157
    56022020 VK170
    55926579 VK386
    55924003 VK358
    55840145 VK145
    55753255 VK151
    55687112 VK330
    55660997 VK536
    55538041 VK53
    55071560 VK335
    55020196 VK259
    54721389 VK482
    54655886 VK369
    54267215 VK400
    54265541 VK165
    54250227 VK111
    54224002 VK392
    54022293 VK405
    53867663 VK205
    53393101 VK344
    53207257 VK477
    53166662 VK15
    52562669 VK177
    52450592 VK143
    52237024 VK123
    52208552 VK261
    52153862 VK150
    51959065 VK284
    51692625 VK525
    51657859 VK488
    51515663 VK56
    51360636 VK492
    51274903 VK388
    50819629 VK527
    50759246 VK291
    50204816 VK373
    49891554 VK257
    49518903 VK35
    49476304 VK245
    48751203 VK264
    48012074 VK187
    47971093 VK33
    47946129 VK258
    47527084 VK348
    47375073 VK367
    47178684 VK554
    46939415 VK306
    46623849 VK156
    46261355 VK174
    46139571 VK69
    46073047 VK517
    45975509 VK204
    44651721 VK480
    44539847 VK266
    44402287 VK260
    44325340 VK127
    44116249 VK543
    43645240 VK167
    43188206 VK530
    43149889 VK504
    43026890 VK490
    42887682 VK175
    41950505 VK394
    41646587 VK108
    41175141 VK147
    41062221 VK178
    40952665 VK540
    40898656 VK444
    40846179 VK507
    38755140 VK241
    37687643 VK288
    37388727 VK289
    37154975 VK286
    37007545 VK64
    36754010 VK51
    36526373 VK19
    36186456 VK301
    35632340 VK365
    33987946 VK18
    33771507 VK278
    33355143 VK186
    33301649 VK297
    33211698 VK366
    32281936 VK485
    32182127 VK240
    32164497 VK325
    32083104 VK354
    32071005 VK234
    31694180 VK207
    31363253 VK60
    30986526 VK371
    30587758 VK340
    30003367 VK285
    29688074 VK242
    29683404 VK362
    29432705 VK515
    29213860 VK134
    28774073 VK334
    28510687 VK295
    28418303 VK315
    28107120 VK218
    27528077 VK319
    26745716 VK338
    26499893 VK296
    26284597 VK183
    26105388 VK225
    25581693 VK254
    24821769 VK287
    24654785 VK244
    24404237 VK17
    24271262 VK227
    24181973 VK139
    23992094 VK300
    23942105 VK518
    22860106 VK20
    22692715 VK65
    22370232 VK30
    22196999 VK138
    22069318 VK282
    21832445 VK275
    21569270 VK44
    21358942 VK391
    20874970 VK31
    20477880 VK223
    19514234 VK298
    18835669 VK48
    18024684 VK312
    17747470 VK212
    16425771 VK232
    16397844 VK92
    15819584 VK23
    15600276 VK159
    15512744 VK280
    15432776 VK224
    15171702 VK90
    15156008 VK314
    14933941 VK313
    14217405 VK27
    13883660 VK309
    13848736 VK75
    13816804 VK432
    13138348 VK117
    13007978 VK460
    12775725 VK434
    12768226 VK454
    12331444 VK431
    12215656 VK461
    12204233 VK463
    11710645 VK452
    11420930 VK438
    11381933 VK71
    11271278 VK430
    11205000 VK407
    10897617 VK16
    10891974 VK155
    10745337 VK469
    10446486 VK471
    10392406 VK519
    10375293 VK63
    10350992 VK408
    10310741 VK272
    10140147 VK459
    10071107 VK428
    10023786 VK457
    9964552 VK57
    9692365 VK458
    9619018 VK214
    9065938 VK21
    8833321 VK409
    8784900 VK268
    8706076 VK24
    8625976 VK453
    8572237 VK124
    8551515 VK114
    7872167 VK14
    7688870 VK494
    7410379 VK22
    7224679 VK217
    7165667 VK579
    7150649 VK439
    7027695 VK171
    6996282 VK94
    6736440 VK39
    6713219 VK466
    6538989 VK424
    6535029 VK45
    6451994 VK426
    6434708 VK425
    6428562 VK450
    6414252 VK144
    6301176 VK410
    6144025 VK113
    6015331 VK380
    5713677 VK276
    5472070 VK213
    5375861 VK427
    5357669 VK476
    5284087 VK582
    4999231 VK292
    4642827 VK211
    4595339 VK11
    4058891 VK546
    4041281 VK9
    3995941 VK248
    3966170 VK462
    3875112 VK255
    3787269 VK269
    3533294 VK464
    3528791 VK267
    3399771 VK440
    3151297 VK215
    3144405 VK472
    3102520 VK379
    3012908 VK189
    3008248 VK208
    2960160 VK247
    2957268 VK153
    2787619 VK193
    2722991 VK435
    2704177 VK158
    2679975 VK382
    2667755 VK228
    2509141 VK210
    2470080 VK270
    2364754 VK196
    2263157 VK251
    2218845 VK383
    2161346 VK226
    2080386 VK148
    1779626 VK216
    1740576 VK133
    1705977 VK78
    1642701 VK191
    1597557 VK413
    1506196 VK441
    1411000 VK239
    1284128 VK470
    1149522 VK161
    1066220 VK437
    980131 VK163
    923511 VK411
    909216 VK200
    802645 VK347
    704789 VK421
    699554 VK140
    696430 VK467
    684764 VK339
    628276 VK182
    611120 VK180
    528230 VK304
    500719 VK86
    495142 VK206
    476715 VK135
    471158 VK253
    427312 VK149
    368739 VK77
    315992 VK359
    304321 VK116
    213728 VK74
    176829 VK252
    171821 VK76
    163898 VK318
    151154 VK185
    140996 VK125
    104116 VK164
    86661 VK222

  12. #787
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    55
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    Ethnicity
    Colonial American
    Nationality
    Tennessean
    Y-DNA (P)
    J-Y150765
    mtDNA (M)
    H1j4

    United States of America
    Yleaf gives VK333 DF19* (xL1199, S233). I'll give him a look in Integrative Genomics Viewer tomorrow unless someone else beats me to it
    Predominantly Appalachian, Middle TN, and North GA roots

    Y-DNA in BR2's branch J-Z30682 (under M172, M67, Z7671, and Y11200). Interested in Z7671 and other J2 in the Caucasus

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     Dewsloth (09-17-2020)

  14. #788
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    Finnish
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    R1b-Z142
    mtDNA (M)
    H10g

    Göran Runström stated on Facebook: "FTDNA is downloading and processing these results right now so we should start seeing the first ancient/modern pair branches on the haplotree in a few days."

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  16. #789
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    91
    Sex
    Location
    Canada
    Y-DNA (P)
    R-S190
    mtDNA (M)
    U5a1

    Canada United States of America Scotland Poland
    I've taken a look at a couple kits. I plan on looking at more of them. The data is sparse, but seems fairly clean.

    For VK242 I have R-L21>L1335>L1065>Z16325>S744>S764. He's positive for CTS11722 (1T), S743 (1C) and S7370 (1T).

    For VK386 I have R-L21>L1335>L1065>Z16325>S744>S691>S695. He's positive for S744 (1A), S695 (1G) and BY3145/BY3126 (1C).

    I may come back and investigate these men more in the future. There are many downstream branches that can't be ruled out.

  17. The Following 10 Users Say Thank You to Williamson For This Useful Post:

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  18. #790
    Registered Users
    Posts
    726

    If anyone with the technological know how could look at VK521 for me and let me know if this sample has any positive reads for SNPs downstream of I-Z2040 it would be much appreciated
    Haplogroup I > I1 > DF29 >
    Z58 > Z59 > Z2041 > Z2040 >
    Z382 > S26361 > S16414 >
    FGC24354 > FGC24357 > FGC24356 >
    S10350 > FGC75802 > Y125947 >
    S21197 Netherlands > BY149414 Scotland >
    BY188003 Belgium > BY188570 Belgium

    YFull id: YF68407

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