Table 2 Read statistics of the reference genome.

Raw reads

135,067,560

100,031,546

119,844,714

110,990,304

122,657,326

136,969,360

Total reads

101,734,214

76,072,598

82,901,000

82,165,530

88,819,554

93,869,100

Total number of reads mapped

78,625,843 (77.29%)

58,935,848 (77.47%)

62,008,068 (74.80%)

60,455,546 (73.58%)

67,337,265 (75.81%)

69,827,122 (74.39%)

Number of reads that mapped to multiple regions

3,792,793 (3.73%)

2,606,663 (3.43%)

3,322,008 (4.01%)

3,470,863 (4.22%)

3,937,078 (4.43%)

3,997,927 (4.26%)

Number of reads that were mapped to unique regions

74,833,050 (73.56%)

56,329,185 (74.05%)

58,686,060 (70.79%)

56,984,683 (69.35%)

63,400,187 (71.38%)

65,829,195 (70.13%)

Read-1

38,037,308 (37.39%)

286,21,024 (37.62%)

29,752,817 (35.89%)

28,436,715 (34.61%)

32,177,909 (36.23%)

33,403,729 (35.59%)

Read-2

36,795,742 (36.17%)

27,708,161 (36.42%)

28,933,243 (34.90%)

28,547,968 (34.74%)

31,222,278 (35.15%)

32,425,466 (34.54%)

Number of reads that map to ‘+’

37,435,639 (36.80%)

28,177,639 (37.04%)

29,369,825 (35.43%)

28,554,241 (34.75%)

31,731,741 (35.73%)

32,953,615 (35.11%)

Number of reads map to ‘−’

37,397,411 (36.76%)

28,151,546 (37.01%)

29,16,235 (35.36%)

28,430,442 (34.60%)

31,668,446 (35.65%)

32,875,580 (35.02%)

Number of non-splice reads

65,956,768 (64.83%)

50,126,819 (65.89%)

50,492,679 (60.91%)

48,280,120 (58.76%)

54,077,425 (60.88%)

56,555,536 (60.25%)

Number of splice reads

8,876,282 (8.72%)

6,202,366 (8.15%)

8,193,381 (9.88%)

8,704,563 (10.59%)

9,322,762 (10.50%)

9,273659 (9.88%)

Number of reads mapped in proper pairs

66,749,602 (65.61%)

50,161,962 (65.94%)

51,970,094 (62.69%)

51,198,774 (62.31%)

56,791,332 (63.94%)

58,971,888 (62.82%)