Немного про качество импьюта от Г...
Начнем с vcf
В этом году они начали его импьютировать, если не знали
Сравнение с вполне приличным тестом от ftdna. Когда будет 30X повторим с максимальной точностью
SNPs file 1: 630 074
SNPs file 2: 493 163
SNPs in common: 436 469
SNPs that are present in File 1 but absent in File 2: 192 824
SNPs that are present in File 2 but absent in File 1: 56 694
No-Calls in File 1: 1 725
No-Calls in File 2: 00
The total number of SNPs that were not considered due to No-Calls: 1 725
GENOTYPE ANALYSIS IN COMMON SNPS
--------------------------------
Full equal genotypes...................: 432 773 (99,55%)
Half equal genotypes...................: 1 874 (0,43%)
Not equal genotypes....................: 97 (0,02%)
DETAIL BY CHROMOSOME
--------------------
Average of full equal genotypes.: 16 645
Average of half-equal genotypes.: 72
Average of not equal genotypes..: 04
> Chromosome 1
Full equal genotypes.: 33 487 (99,58%)
Half equal genotypes.: 138 (0,41%)
Not equal genotypes..: 03 (0,01%)
> Chromosome 2
Full equal genotypes.: 34 246 (99,67%)
Half equal genotypes.: 107 (0,31%)
Not equal genotypes..: 08 (0,02%)
> Chromosome 3
Full equal genotypes.: 33 125 (99,56%)
Half equal genotypes.: 138 (0,41%)
Not equal genotypes..: 10 (0,03%)
> Chromosome 4
Full equal genotypes.: 30 426 (99,59%)
Half equal genotypes.: 118 (0,39%)
Not equal genotypes..: 06 (0,02%)
> Chromosome 5
Full equal genotypes.: 28 489 (99,54%)
Half equal genotypes.: 126 (0,44%)
Not equal genotypes..: 06 (0,02%)
> Chromosome 6
Full equal genotypes.: 34 172 (99,49%)
Half equal genotypes.: 167 (0,49%)
Not equal genotypes..: 09 (0,03%)
> Chromosome 7
Full equal genotypes.: 26 273 (99,55%)
Half equal genotypes.: 112 (0,42%)
Not equal genotypes..: 07 (0,03%)
> Chromosome 8
Full equal genotypes.: 24 400 (99,51%)
Half equal genotypes.: 113 (0,46%)
Not equal genotypes..: 07 (0,03%)
> Chromosome 9
Full equal genotypes.: 14 765 (99,56%)
Half equal genotypes.: 62 (0,42%)
Not equal genotypes..: 03 (0,02%)
> Chromosome 10
Full equal genotypes.: 23 568 (99,47%)
Half equal genotypes.: 123 (0,52%)
Not equal genotypes..: 03 (0,01%)
> Chromosome 11
Full equal genotypes.: 23 674 (99,52%)
Half equal genotypes.: 108 (0,45%)
Not equal genotypes..: 06 (0,03%)
> Chromosome 12
Full equal genotypes.: 18 773 (99,58%)
Half equal genotypes.: 77 (0,41%)
Not equal genotypes..: 03 (0,02%)
> Chromosome 13
Full equal genotypes.: 13 726 (99,66%)
Half equal genotypes.: 47 (0,34%)
Not equal genotypes..: 00 (0%)
> Chromosome 14
Full equal genotypes.: 11 820 (99,56%)
Half equal genotypes.: 49 (0,41%)
Not equal genotypes..: 03 (0,03%)
> Chromosome 15
Full equal genotypes.: 11 177 (99,66%)
Half equal genotypes.: 35 (0,31%)
Not equal genotypes..: 03 (0,03%)
> Chromosome 16
Full equal genotypes.: 11 838 (99,65%)
Half equal genotypes.: 39 (0,33%)
Not equal genotypes..: 02 (0,02%)
> Chromosome 17
Full equal genotypes.: 10 601 (99,58%)
Half equal genotypes.: 43 (0,4%)
Not equal genotypes..: 02 (0,02%)
> Chromosome 18
Full equal genotypes.: 10 778 (99,51%)
Half equal genotypes.: 51 (0,47%)
Not equal genotypes..: 02 (0,02%)
> Chromosome 19
Full equal genotypes.: 7 935 (99,51%)
Half equal genotypes.: 38 (0,48%)
Not equal genotypes..: 01 (0,01%)
> Chromosome 20
Full equal genotypes.: 9 038 (99,45%)
Half equal genotypes.: 50 (0,55%)
Not equal genotypes..: 00 (0%)
> Chromosome 21
Full equal genotypes.: 5 156 (99,75%)
Half equal genotypes.: 12 (0,23%)
Not equal genotypes..: 01 (0,02%)
> Chromosome 22
Full equal genotypes.: 5 318 (99,53%)
Half equal genotypes.: 25 (0,47%)
Not equal genotypes..: 00 (0%)
> Chromosome X
Full equal genotypes.: 9 988 (98,93%)
Half equal genotypes.: 96 (0,95%)
Not equal genotypes..: 12 (0,12%)
> Chromosome Y
No info
> Chromosome MT
No info
SNPs WITH IDENTICAL GENOTYPES
-----------------------------
CC: 103 432
GG: 103 002
TT: 77 530
AA: 77 378
CT: 28 973
AG: 28 556
AC: 6 726
GT: 6 721
CG: 276
AT: 179
В целом правило <0.5% выдерживается, кроме X
На всякий случай проверим их импьют V5 по сравнению с vcf
SNPs file 1: 628 674
SNPs file 2: 493 163
SNPs in common: 474 950
SNPs that are present in File 1 but absent in File 2: 153 724
SNPs that are present in File 2 but absent in File 1: 18 213
No-Calls in File 1: 379
No-Calls in File 2: 00
The total number of SNPs that were not considered due to No-Calls: 379
GENOTYPE ANALYSIS IN COMMON SNPS
--------------------------------
Full equal genotypes...................: 473 595 (99,79%)
Half equal genotypes...................: 409 (0,09%)
Not equal genotypes....................: 567 (0,12%)
DETAIL BY CHROMOSOME
--------------------
Average of full equal genotypes.: 18 215
Average of half-equal genotypes.: 16
Average of not equal genotypes..: 22
> Chromosome 1
Full equal genotypes.: 37 365 (99,9%)
Half equal genotypes.: 31 (0,08%)
Not equal genotypes..: 06 (0,02%)
> Chromosome 2
Full equal genotypes.: 39 062 (99,92%)
Half equal genotypes.: 20 (0,05%)
Not equal genotypes..: 13 (0,03%)
> Chromosome 3
Full equal genotypes.: 32 840 (99,91%)
Half equal genotypes.: 26 (0,08%)
Not equal genotypes..: 05 (0,02%)
> Chromosome 4
Full equal genotypes.: 30 188 (99,88%)
Half equal genotypes.: 30 (0,1%)
Not equal genotypes..: 05 (0,02%)
> Chromosome 5
Full equal genotypes.: 28 305 (99,88%)
Half equal genotypes.: 29 (0,1%)
Not equal genotypes..: 04 (0,01%)
> Chromosome 6
Full equal genotypes.: 33 958 (99,91%)
Half equal genotypes.: 27 (0,08%)
Not equal genotypes..: 05 (0,01%)
> Chromosome 7
Full equal genotypes.: 25 889 (99,91%)
Half equal genotypes.: 20 (0,08%)
Not equal genotypes..: 03 (0,01%)
> Chromosome 8
Full equal genotypes.: 24 334 (99,85%)
Half equal genotypes.: 25 (0,1%)
Not equal genotypes..: 11 (0,05%)
> Chromosome 9
Full equal genotypes.: 20 120 (99,92%)
Half equal genotypes.: 13 (0,06%)
Not equal genotypes..: 03 (0,01%)
> Chromosome 10
Full equal genotypes.: 23 391 (99,9%)
Half equal genotypes.: 23 (0,1%)
Not equal genotypes..: 00 (0%)
> Chromosome 11
Full equal genotypes.: 23 395 (99,91%)
Half equal genotypes.: 14 (0,06%)
Not equal genotypes..: 06 (0,03%)
> Chromosome 12
Full equal genotypes.: 22 264 (99,86%)
Half equal genotypes.: 26 (0,12%)
Not equal genotypes..: 06 (0,03%)
> Chromosome 13
Full equal genotypes.: 16 865 (99,69%)
Half equal genotypes.: 14 (0,08%)
Not equal genotypes..: 39 (0,23%)
> Chromosome 14
Full equal genotypes.: 14 824 (99,93%)
Half equal genotypes.: 08 (0,05%)
Not equal genotypes..: 03 (0,02%)
> Chromosome 15
Full equal genotypes.: 14 247 (99,89%)
Half equal genotypes.: 11 (0,08%)
Not equal genotypes..: 05 (0,04%)
> Chromosome 16
Full equal genotypes.: 15 115 (99,87%)
Half equal genotypes.: 19 (0,13%)
Not equal genotypes..: 01 (0,01%)
> Chromosome 17
Full equal genotypes.: 13 436 (99,67%)
Half equal genotypes.: 14 (0,1%)
Not equal genotypes..: 31 (0,23%)
> Chromosome 18
Full equal genotypes.: 13 674 (99,9%)
Half equal genotypes.: 12 (0,09%)
Not equal genotypes..: 02 (0,01%)
> Chromosome 19
Full equal genotypes.: 9 832 (99,86%)
Half equal genotypes.: 13 (0,13%)
Not equal genotypes..: 01 (0,01%)
> Chromosome 20
Full equal genotypes.: 11 223 (99,83%)
Half equal genotypes.: 16 (0,14%)
Not equal genotypes..: 03 (0,03%)
> Chromosome 21
Full equal genotypes.: 6 464 (99,89%)
Half equal genotypes.: 07 (0,11%)
Not equal genotypes..: 00 (0%)
> Chromosome 22
Full equal genotypes.: 6 341 (99,84%)
Half equal genotypes.: 07 (0,11%)
Not equal genotypes..: 03 (0,05%)
> Chromosome X
Full equal genotypes.: 10 260 (99,79%)
Half equal genotypes.: 04 (0,04%)
Not equal genotypes..: 18 (0,18%)
> Chromosome Y
No info
> Chromosome MT
Full equal genotypes.: 203 (34%)
Half equal genotypes.: 00 (0%)
Not equal genotypes..: 394 (66%)
SNPs WITH IDENTICAL GENOTYPES
-----------------------------
CC: 112 487
GG: 112 141
AA: 84 785
TT: 84 732
CT: 16 172
TC: 15 934
AG: 15 868
GA: 15 727
CA: 3 798
TG: 3 778
AC: 3 770
GT: 3 737
GC: 144
CG: 138
TA: 94
AT: 87
A: 75
T: 55
C: 40
G: 33
Все понятно, безобразие только с MT
Ну и наконец сравниваем V5 с ftdna
SNPs file 1: 628 674
SNPs file 2: 630 074
SNPs in common: 545 028
SNPs that are present in File 1 but absent in File 2: 83 646
SNPs that are present in File 2 but absent in File 1: 85 046
No-Calls in File 1: 28 294
No-Calls in File 2: 4 273
The total number of SNPs that were not considered due to No-Calls: 30 638
GENOTYPE ANALYSIS IN COMMON SNPS
--------------------------------
Full equal genotypes...................: 506 423 (98,45%)
Half equal genotypes...................: 7 259 (1,41%)
Not equal genotypes....................: 708 (0,14%)
DETAIL BY CHROMOSOME
--------------------
Average of full equal genotypes.: 19 478
Average of half-equal genotypes.: 279
Average of not equal genotypes..: 27
> Chromosome 1
Full equal genotypes.: 38 755 (98,83%)
Half equal genotypes.: 436 (1,11%)
Not equal genotypes..: 21 (0,05%)
> Chromosome 2
Full equal genotypes.: 39 972 (98,84%)
Half equal genotypes.: 450 (1,11%)
Not equal genotypes..: 20 (0,05%)
> Chromosome 3
Full equal genotypes.: 38 901 (98,83%)
Half equal genotypes.: 440 (1,12%)
Not equal genotypes..: 19 (0,05%)
> Chromosome 4
Full equal genotypes.: 35 965 (98,53%)
Half equal genotypes.: 506 (1,39%)
Not equal genotypes..: 31 (0,08%)
> Chromosome 5
Full equal genotypes.: 33 319 (98,57%)
Half equal genotypes.: 452 (1,34%)
Not equal genotypes..: 31 (0,09%)
> Chromosome 6
Full equal genotypes.: 39 581 (98,42%)
Half equal genotypes.: 604 (1,5%)
Not equal genotypes..: 30 (0,07%)
> Chromosome 7
Full equal genotypes.: 30 937 (98,66%)
Half equal genotypes.: 407 (1,3%)
Not equal genotypes..: 12 (0,04%)
> Chromosome 8
Full equal genotypes.: 28 663 (98,48%)
Half equal genotypes.: 425 (1,46%)
Not equal genotypes..: 16 (0,05%)
> Chromosome 9
Full equal genotypes.: 17 289 (98,88%)
Half equal genotypes.: 184 (1,05%)
Not equal genotypes..: 11 (0,06%)
> Chromosome 10
Full equal genotypes.: 27 507 (97,95%)
Half equal genotypes.: 527 (1,88%)
Not equal genotypes..: 49 (0,17%)
> Chromosome 11
Full equal genotypes.: 27 370 (98,46%)
Half equal genotypes.: 402 (1,45%)
Not equal genotypes..: 26 (0,09%)
> Chromosome 12
Full equal genotypes.: 21 939 (98,66%)
Half equal genotypes.: 288 (1,3%)
Not equal genotypes..: 10 (0,04%)
> Chromosome 13
Full equal genotypes.: 15 857 (98,73%)
Half equal genotypes.: 189 (1,18%)
Not equal genotypes..: 15 (0,09%)
> Chromosome 14
Full equal genotypes.: 13 993 (98,05%)
Half equal genotypes.: 261 (1,83%)
Not equal genotypes..: 17 (0,12%)
> Chromosome 15
Full equal genotypes.: 13 081 (98,88%)
Half equal genotypes.: 140 (1,06%)
Not equal genotypes..: 08 (0,06%)
> Chromosome 16
Full equal genotypes.: 13 903 (98,71%)
Half equal genotypes.: 177 (1,26%)
Not equal genotypes..: 05 (0,04%)
> Chromosome 17
Full equal genotypes.: 12 448 (98,23%)
Half equal genotypes.: 214 (1,69%)
Not equal genotypes..: 10 (0,08%)
> Chromosome 18
Full equal genotypes.: 12 607 (98,38%)
Half equal genotypes.: 200 (1,56%)
Not equal genotypes..: 07 (0,05%)
> Chromosome 19
Full equal genotypes.: 9 495 (97,88%)
Half equal genotypes.: 198 (2,04%)
Not equal genotypes..: 08 (0,08%)
> Chromosome 20
Full equal genotypes.: 10 619 (98,23%)
Half equal genotypes.: 184 (1,7%)
Not equal genotypes..: 07 (0,06%)
> Chromosome 21
Full equal genotypes.: 6 053 (98,57%)
Half equal genotypes.: 86 (1,4%)
Not equal genotypes..: 02 (0,03%)
> Chromosome 22
Full equal genotypes.: 6 319 (98,12%)
Half equal genotypes.: 117 (1,82%)
Not equal genotypes..: 04 (0,06%)
> Chromosome X
Full equal genotypes.: 11 850 (94,26%)
Half equal genotypes.: 372 (2,96%)
Not equal genotypes..: 349 (2,78%)
> Chromosome Y
No info
> Chromosome MT
No info
SNPs WITH IDENTICAL GENOTYPES
-----------------------------
CC: 121 287
GG: 121 021
TT: 90 909
AA: 90 782
CT: 16 785
AG: 16 637
TC: 16 586
GA: 16 413
CA: 3 916
TG: 3 900
AC: 3 872
GT: 3 820
GC: 152
CG: 147
TA: 100
AT: 96
Стандартные 1.5% неправильного импьюта, на некоторых хромосомах больше, совсем все плохо на X
Это видно на совпадениях по X в gedmatch и ftdna
Тема: Генотек (Прочитано 150527 раз)