Validation of rice genome sequence by optical mapping

BMC Genomics

Table 1 Rice (Oryza sativa ssp. japonica cv. Nipponbare) whole-genome shotgun optical mapping

Ch.	Est. Size (Mb) YAC^a	Est. Size (Mb) BAC^b	FISH^c Size(Mb)/AR	IRGSP^d	Opt. Map Contig (status)	Opt. Map (Mb)	Predicted Size (Mb)^e/ArmRatio	Difference (%) YAC/BAC/FISH/IRGSP	Ave. frag. size (kb)	# of Mol.	X Cov.	Ave. frag. size SD (kb)
1	51.5	44	56.9/1.63	45.05	1(F)	43.66	43.73/1.61	17.77/0.62/30.12/3.02	15.86	3,311	40.48	1.44
2	43.4	39.8	48.8/1.68	36.78	1(F)	36.14	36.21/1.62	19.86/9.91/34.77/1.57	15.15	2,456	35.69	1.47
3	47.5	40.8	52.5/0.89	37.37	1(F)	36.97	37.03/0.84	28.27/10.18/41.78/0.92	15.30	2,669	39.38	1.46
4	36.8	39	35.5/5.13	36.15	1(F)	35.80	35.85/2.61	2.65/8.79/0.98/0.84	14.55	2,368	35.38	1.39
5	33.6	33.2	34.6/1.99	30.00	1(F)	30.06	30.11/1.44	11.59/10.26/14.91/0.37	14.30	1,845	33.03	1.40
6	35.1	31.8	35.7/0.93	31.60	1	16.09	31.94/1.01	9.89/0.44/11.77/1.06	13.99	1,536	47.03	1.37
					2	15.78			14.89	1,483	44.17	1.40
7	33.1	35	32.3/1.78	30.28	1(F)	29.65	29.71/1.45	11.41/17.81/8.72/1.92	14.41	2,052	35.93	1.37
8	33.6	27.6	30.0/1.38	28.56	1(F)	28.40	28.45/1.09	18.10/2.99/5.45/0.39	13.46	2,244	39.38	1.37
9	27	21.6	26.7/6.54	30.53	1	24.50	26.53/2.77	1.77/18.58/0.64/15.08	14.16	2,112	39.19	1.48
10	23.7	26.8	23.0/3.07	23.96	1(F)	23.96	24.00/1.85	1.25/11.67/4.17/0.17	13.12	2,658	55.74	1.32
11	33.7	30.3	28.8/1.32	30.76	1	17.21	31.00/1.39	8.71/2.26/7.10/0.77	14.34	1,202	35.38	1.34
					2	12.37			14.11	931	35.55	1.39
12	30.9	30.6	25.1/1.32	27.77	1(F)	28.19	28.24/1.22	9.42/8.36/11.12/1.66	14.07	2,645	45.38	1.27
Total	430	400.5	430	388.82	14	378.31	382.80/NA	12.33/4.62/12.33/1.57		29,512
Ave.									14.41		40.12	1.39

*Ch. = Ch romosome; est. = est imated; AR = A rm R atio; Opt. = Opt ical; Ave. = Ave rage; Frag. = Frag ment; SD = S tandard D eviation; Cov. = Cov erage; F = F inished; Difference = |Estimated size-Optical Map size|/Optical Map size*100%; Mol. No.: the number of single molecule maps were used to build the chromosome optical map contig; X Cov erage = (total mass of maps within a contig)/(chromosome optical map consensus size). ^a Estimated chromosome size is based on the YAC and BAC physical map [7]; ^b Estimated chromosome size is based on the BAC/PAC physical map [13]; ^c Estimated chromosome size by pachytene FISH [62]. ^d International Rice Genome Sequencing Project [37]. ^ePredicted chromosome size = the optical map sizes + gap sizes [the centromere sizes in BAC and YAC map for chromosome 6 and 11] + missing small fragment sizes (Table 2).

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