Skip to main content

Table 3 Coverage and number of effective sites for detection of variation

From: Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data

Chr

length (bp)a

NIAS

CSHL

NIAS + CSHL

Covb (%)

Effc (%)

Cov (%)

Eff (%)

Cov (%)

Eff (%)

chr01

43,270,899

35,791,098 (82.7%)

18,246,140 (42.2%)

39,956,568 (92.3%)

38,068,615 (88.0%)

39,961,540 (92.4%)

38,175,168 (88.2%)

chr02

35,937,247

30,154,356 (83.9%)

15,638,850 (43.5%)

33,524,321 (93.3%)

32,062,712 (89.2%)

33,528,628 (93.3%)

32,148,332 (89.5%)

chr03

36,413,819

31,059,089 (85.3%)

15,977,692 (43.9%)

34,365,834 (94.4%)

32,996,819 (90.6%)

34,369,143 (94.4%)

33,082,516 (90.9%)

chr04

35,502,790

26,736,290 (75.3%)

12,921,248 (36.4%)

31,176,439 (87.8%)

29,064,227 (81.9%)

31,186,864 (87.8%)

29,153,050 (82.1%)

chr05

29,958,438

23,400,797 (78.1%)

11,810,143 (39.4%)

26,853,884 (89.6%)

25,256,988 (84.3%)

26,857,426 (89.6%)

25,327,281 (84.5%)

chr06

31,248,789

24,651,481 (78.9%)

12,398,636 (39.7%)

28,084,165 (89.9%)

26,516,110 (84.9%)

28,088,052 (89.9%)

26,594,708 (85.1%)

chr07

29,697,629

23,447,981 (79.0%)

11,725,346 (39.5%)

26,880,079 (90.5%)

25,363,522 (85.4%)

26,883,654 (90.5%)

25,438,043 (85.7%)

chr08

28443,027

22,122,986 (77.8%)

11,013,746 (38.7%)

25,508,624 (89.7%)

23,953,312 (84.2%)

25,512,422 (89.7%)

24,024,380 (84.5%)

chr09

23,012,721

18,240,332 (79.3%)

9,052,990 (39.3%)

20,858,168 (90.6%)

19,681,323 (85.5%)

20,860,908 (90.6%)

19,739,054 (85.8%)

chr10

23,208,246

18,119,906 (78.1%)

8,873,977 (38.2%)

20,931,379 (90.2%)

19,673,976 (84.8%)

20,934,165 (90.2%)

19,732,853 (85.0%)

chr11

29,021,139

22,586,659 (77.8%)

11,082,625 (38.2%)

25,987,560 (89.5%)

24,468,775 (84.3%)

25,990922 (89.6%)

24,546,522 (84.6%)

chr12

27,531,905

20,923,037 (76.0%)

10,270,579 (37.3%)

24,427,691 (88.7%)

22,818,854 (82.9%)

24,432,616 (88.7%)

22,891,243 (83.1%)

Total

373,246,649

297,234,012 (79.6%)

149,011,972 (39.9%)

338,554,712 (90.7%)

31,9925,233 (85.7%)

338,606,340 (90.7%)

320,853,150 (86.0%)

  1. a Length before error correction.
  2. b Cov: Number of sites covered with at least one read.
  3. c Eff: Number of effective sites covered with at least 10 high quality (base quality ≥20) reads.