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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.