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Table 1 Summary of read mapping for RNA-seq

From: Transcriptomic comparison between developing seeds of yellow- and black-seeded Brassica napus reveals that genes influence seed quality

Sample name

B3

B4

B5

B6

BM

Y3

Y4

Y5

Y6

YM

Raw reads

47,536,866

42,753,820

44,341,556

51,507,518

51,272,946

48,704,282

45,694,038

44,797,562

45,996,584

52,804,244

Clean reads

45,555,018

41,801,216

40,620,518

43,833,034

48,665,348

46,813,976

43,798,322

42,843,336

43,736,106

50,268,482

Total mapped

36,499,205 (80.12%)

34,214,293 (81.85%)

32,844,328 (80.86%)

35,032,820 (79.92%)

39,325,179 (80.81%)

38,116,991 (81.42%)

35,893,586 (81.95%)

35,376,347 (82.57%)

36,029,106 (82.38%)

40,839,634 (81.24%)

Multiple mapped

2,175,877 (4.78%)

2,332,136 (5.58%)

2,561,972 (6.31%)

3,271,514 (7.46%)

3,151,365 (6.48%)

2,327,452 (4.97%)

2,287,911 (5.22%)

2,274,889 (5.31%)

2,451,932 (5.61%)

3,198,280 (6.36%)

Uniquely mapped

34,323,328 (75.34%)

31,882,157 (76.27%)

30,282,356 (74.55%)

31,761,306 (72.46%)

36,173,814 (74.33%)

35,789,539 (76.45%)

33,605,675 (76.73%)

33,101,458 (77.26%)

33,577,174 (76.77%)

37,641,354 (74.88%)

Reads map to ‘+’

17,137,064 (37.62%)

15,873,247 (37.97%)

15,138,033 (37.27%)

15,900,632 (36.28%)

18,123,297 (37.24%)

17,872,927 (38.18%)

16,769,787 (38.29%)

16,508,902 (38.53%)

16,764,771 (38.33%)

18,866,098 (37.53%)

Reads map to ‘-’

17,186,264 (37.73%)

16,008,910 (38.3%)

15,144,323 (37.28%)

15,860,674 (36.18%)

18,050,517 (37.09%)

17,916,612 (38.27%)

16,835,888 (38.44%)

16,592,556 (38.73%)

16,812,403 (38.44%)

18,775,256 (37.35%)

Non-splice reads

21,266,684 (46.68%)

21,368,313 (51.12%)

21,381,177 (52.64%)

22,323,651 (50.93%)

24,534,251 (50.41%)

22,491,873 (48.05%)

22,291,894 (50.9%)

24,114,006 (56.28%)

24,559,779 (56.15%)

26,061,989 (51.85%)

Splice reads

13,056,644 (28.66%)

10,513,844 (25.15%)

8,901,179 (21.91%)

9,437,655 (21.53%)

11,639,563 (23.92%)

13,297,666 (28.41%)

11,313,781 (25.83%)

8,987,452 (20.98%)

9,017,395 (20.62%)

11,579,365 (23.04%)

  1. B3, B4, B5, B6 and BM indicate 3 ~ 6 WAF and mature black seed. Y3, Y4, Y5, Y6 and YM indicate 3 ~ 6 WAF and mature yellow seed