Validation of rice genome sequence by optical mapping

BMC Genomics

Table 2 Comparison between the optical maps and the in silico maps from the IRGSP pseudomolecules of rice genome sequence

					IRGSP sequence pseudomolecule					Optical map
Ch.	# Match frag.	Total match frag. mass (Mb)	Percent (%) out of total mass^a	Ave. frag. relative sizing error(%)	# Telomeric gap/mass (kb)	Centr. gap mass (kb)	# Gaps Filling/Mass (kb)	# Gaps Calling/mass (kb)	# Misassembly/Mass (kb)	# Missing small frag./mass (kb)	# Missing/false cut(s)
1	2605	42.22	96.70	3.30	2/12	1/707	5/69	6/42	3/57	87/66.38	43/4
2	2272	35.23	97.48	3.41	1/6	1/429	3/21	2/12	2/10	73/65.55	27/1
3	2312	36.75	99.40	3.37	2/37	1/438	4/496	7/75	4/239	74/63.74	45/4
4	2230	33.65	93.99	3.49	2/111	0/0	5/192	15/359	15/1036	63/51.45	36/5
5	1985	29.03	96.57	3.60	2/255	1/54	5/96	9/66	8/314	61/52.26	29/3
6	2114	30.84	96.56	3.34	2/175	1/810	2/12	3/17	1/36	80/68.71	40/5
7	1974	29.20	98.48	3.60	1/13	2/84	0/0	8/145	3/55	64/57.67	39/4
8	1999	28.00	98.59	3.37	2/16	1/24	0/0	6/104	1/39	59/53.10	30/0
9	1613	22.31	84.25	3.63	2/3503	1/320	3/51	3/16	1/55	59/52.24	42/5
10	1664	22.51	93.95	3.35	2/54	1/117	5/671	7/79	3/62	45/36.53	28/4
11	1892	27.29	88.26	3.60	2/67	1/2090	4/178	9/141	5/635	91/76.07	23/8
12	1844	26.70	94.71	3.41	2/40	1/338	0/0	9/327	7/438	59/46.55	44/2
Total	24,504	363.73			22/4289	12/5240	36/1786	84/1383	53/2974	815/690	426/46
Ave.			94.91	3.46

*Ch. = Ch romosome, Ave. = Ave rage; frag. = frag ment; Centr. = centr omeric; ^a The predicted chromosome size based on optical map was used as the total mass to compute the percentage of the matching fragment mass. Gap or misassembly masses in the alignments were calculated based on the optical mapping data.

ISSN: 1471-2164