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

Yoshihiro Kawahara; Melissa de la Bastide; John P Hamilton; Hiroyuki Kanamori; W Richard McCombie; Shu Ouyang; David C Schwartz; Tsuyoshi Tanaka; Jianzhong Wu; Shiguo Zhou; Kevin L Childs; Rebecca M Davidson; Haining Lin; Lina Quesada-Ocampo; Brieanne Vaillancourt; Hiroaki Sakai; Sung Shin Lee; Jungsok Kim; Hisataka Numa; Takeshi Itoh; C Robin Buell; Takashi Matsumoto

doi:10.1186/1939-8433-6-4

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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
Chr	length (bp)^a	Cov^b (%)	Eff^c (%)	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%)

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

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