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Table 2 Variation detection and annotation

From: A new massively parallel nanoball sequencing platform for whole exome research

   Hiseq-1 Hiseq-2 Hiseq-3 Hiseq-4 BGISEQ-1 BGISEQ-2 BGISEQ-3 BGISEQ-4
SNV total number a 41,554 41,506 41,627 41,540 41,264 41,294 41,292 41,172
found in dbSNP(%) 99.75 99.73 99.70 99.78 99.74 99.76 99.76 99.80
homozygous 15,741 15,723 15,723 15,758 15,671 15,666 15,692 15,642
heterozygous 25,813 25,783 25,904 25,782 25,593 25,628 25,600 25,530
Ti/Tv 2.56 2.57 2.56 2.56 2.56 2.56 2.56 2.56
het/hom b 1.64 1.64 1.65 1.64 1.63 1.64 1.63 1.63
intronic variations c 17,298 17,351 17,321 17,288 17,217 17,232 17,220 17,229
exonic variations 21,540 21,497 21,561 21,533 21,408 21,407 21,433 21,322
coding variations 19,353 19,332 19,354 19,364 19,269 19,273 19,291 19,210
nonsynonmous 9446 9439 9437 9466 9393 9391 9400 9343
Ti/Tv on exome 3.09 3.10 3.08 3.09 3.08 3.08 3.08 3.09
het/hom on exome 1.52 1.52 1.52 1.52 1.52 1.52 1.52 1.52
indel total number 3461 3436 3470 3445 3503 3559 3506 3538
found in dbSNP(%) 94.42 95.08 94.55 94.83 94.78 94.44 94.69 94.04
homozygous 1491 1491 1492 1502 1433 1444 1432 1420
heterozygous 1970 1945 1978 1943 2070 2115 2074 2118
het/hom 1.32 1.30 1.33 1.29 1.44 1.46 1.45 1.49
intronic variations 2493 2493 2518 2496 2558 2585 2553 2581
exonic variations 703 689 702 694 705 706 703 702
coding variations 460 465 459 464 473 477 468 473
het/hom on exome 1.12 1.11 1.11 1.11 1.17 1.21 1.14 1.17
  1. aOnly variants on target region were used in these statistics
  2. bhet/hom, heterozygous to homozygous variation ratio
  3. cVariations located at splicing sites are considered as nonsynonymous and not count as intronic