Table 3:
Variant statistics of Illumina and MGI sequencing platforms
| Metric | HiSeq2000 | HiSeq2500 | HiSeq4000 | HiSeqX10 | NovaSeq6000 | BGISEQ-500 | DNBSEQ-T7 |
|---|---|---|---|---|---|---|---|
| Reference homozygous | 2,839,358,003 | 2,855,619,759 | 2,855,062,233 | 2,864,272,103 | 2,861,198,782 | 2,851,898,568 | 2,853,066,635 |
| No. of no call positions | 80,241,142 | 63,980,549 | 64,532,078 | 55,244,498 | 58,311,103 | 67,747,107 | 66,584,361 |
| No call rate (%) | 2.74 | 2.19 | 2.21 | 1.89 | 1.99 | 2.32 | 2.28 |
| SNVs | |||||||
| Total | 4,133,925 | 4,132,468 | 4,138,296 | 4,216,589 | 4,223,612 | 4,088,645 | 4,082,103 |
| Total in dbSNP | 4,094,212 | 4,114,993 | 4,112,253 | 4,198,005 | 4,184,100 | 4,070,101 | 4,064,986 |
| dbSNP rate (%) | 99.04 | 99.58 | 99.37 | 99.56 | 99.06 | 99.55 | 99.58 |
| Singletons | 159,429 | 78,109 | 98,574 | 100,158 | 104,052 | 52,127 | 51,978 |
| Singletons in dbSNP | 126,762 | 68,673 | 78,361 | 89,094 | 73,177 | 41,092 | 41,743 |
| dbSNP rate for singletons (%) | 79.51 | 87.92 | 79.49 | 88.95 | 70.33 | 78.83 | 80.31 |
| Homozygous | 1,703,616 | 1,690,878 | 1,704,813 | 1,708,639 | 1,714,752 | 1,688,328 | 1,689,834 |
| Heterozygous | 2,430,309 | 2,441,590 | 2,433,483 | 2,507,950 | 2,508,860 | 2,400,317 | 2,392,269 |
| Heterozygous/homozygous ratio | 1.43 | 1.44 | 1.43 | 1.47 | 1.46 | 1.42 | 1.42 |
| Ti/Tv ratio | 1.91 | 1.92 | 1.9 | 1.88 | 1.85 | 1.92 | 1.92 |
| Indels | |||||||
| Total | 526,504 | 546,918 | 491,899 | 689,357 | 708,062 | 703,873 | 631,163 |
| Total in dbSNP | 524,738 | 544,866 | 489,777 | 686,916 | 705,553 | 701,802 | 629,314 |
| dbSNP rate (%) | 99.66 | 99.62 | 99.57 | 99.65 | 99.65 | 99.71 | 99.71 |
| Singletons | 7,864 | 7,444 | 8,094 | 17,036 | 23,596 | 41,384 | 12,092 |
| Singletons in dbSNP | 7,612 | 7,259 | 7,915 | 16,784 | 23,303 | 41,183 | 11,964 |
| dbSNP rate for singletons (%) | 96.80 | 97.51 | 97.79 | 98.52 | 98.76 | 99.51 | 98.94 |