Table 2.
Statistical results of reads versus reference genome alignment.(C1, C2, C3,P1, P2 and P3)
| Sample | C1 | C2 | C3 | P1 | P2 | P3 |
|---|---|---|---|---|---|---|
| Total reads | 100,968,860 | 84,124,574 | 93,671,984 | 112,327,098 | 116,416,902 | 107,328,648 |
| Total mapped reads | 98,410,469(97.47%) | 80,761,974(96.00%) | 90,679,812(96.81%) | 110,381,982(98.27%) | 113,681,744(97.65%) | 105,478,039(98.28%) |
| Multiple mapped | 5,517,703(5.46%) | 11,864,341(14.10%) | 10,680,668(11.40%) | 5,618,803(5.00%) | 5,839,591(5.02%) | 4,908,608(4.57%) |
| Uniquely mapped | 92,892,766(92.00%) | 68,897,633(81.90%) | 79,999,144(85.40%) | 104,763,179(93.27%) | 107,842,153(92.63%) | 100,569,431(93.70%) |
| Read-1 | 46,467,946(46.02%) | 34,482,900(40.99%) | 40,013,656(42.72%) | 52,372,350(46.62%) | 53,907,736(46.31%) | 50,312,496(46.88%) |
| Read-2 | 46,424,820(45.98%) | 34,414,733(40.91%) | 39,985,488(42.69%) | 52,390,829(46.64%) | 53,934,417(46.33%) | 50,256,935(46.83%) |
| Reads map to ‘+’ | 46,449,192(46.00%) | 34,436,432(40.94%) | 40,026,663(42.73%) | 52,388,785(46.64%) | 53,946,432(46.34%) | 50,299,909(46.87%) |
| Reads map to ‘-‘ | 46,443,574(46.00%) | 34,461,201(40.96%) | 39,972,481(42.67%) | 52,374,394(46.63%) | 53,895,721(46.30%) | 50,269,522(46.84%) |
| Non-splice reads | 73,546,464(72.84%) | 55,384,769(65.84%) | 63,325,155(67.60%) | 85,484,277(76.10%) | 89,219,702(76.64%) | 79,552,021(74.12%) |
| Splice reads | 19,346,302(19.16%) | 13,512,864(16.06%) | 16,673,989(17.80%) | 19,278,902(17.16%) | 18,622,451(16.00%) | 21,017,410(19.58%) |
| Reads mapped in proper pairs | 90,007,170(89.14%) | 66,460,176(79.00%) | 77,202,880(82.42%) | 101,626,024(90.47%) | 104,133,722(89.45%) | 98,012,698(91.32%) |