Table 2 Statistical results of reads versus reference genome alignment.(C1, C2, C3,P1, P2 and 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%)