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Table 2 Pairwise concordance of genotype calls between Sanger and array-based methods

From: Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias

  Sanger
MouseDivGeno AA BB Deleted Inaccessible Excluded Total
AA 5,488,489 5,327 88 4,818 3,504 5,502,226
AB 51,460 39,080 24 424 1,316 92,304
BB 7,244 1,627,823 181 3,022 6,230 1,644,500
V 13,510 15,488 24 2,221 4,361 35,604
N 43,605 48,659 19 577 1,588 94,448
Total 5,604,308 1,736,377 336 11,062 16,999 7,369,082
Alchemy AA BB Deleted Inaccessible Excluded Total
AA 5,441,864 3,604 87 4,612 3,262 5,453,429
AB 97,883 46,767 34 553 1,741 146,978
BB 6,582 1,644,208 141 2,231 4,314 1,657,476
N 57,979 41,798 74 3,666 7,682 111,199
Total 5,604,308 1,736,377 336 11,062 16,999 7,369,082
BRLMM-P 2D AA BB Deleted Inaccessible Excluded Total
AA 5,523,440 7,022 63 4,673 3,456 5,538,654
AB 30,970 54,075 70 2,097 4,839 92,051
BB 7,702 1,631,208 169 2,509 5,164 1,646,752
N 42,196 44,072 34 1,783 3,540 91,625
Total 5,604,308 1,736,377 336 11,062 16,999 7,369,082
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