Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

Table 1 Coverage of the Nipponbare Pseudomolecules 4.0 database by the Koshihikari reads from the Solexa Genome Analyzer.

				Uniquely mapped reads
Chromosome	Pseudomolecule of Nipponbare (bp)^a	Koshihikari aligned length (bp)^b	Coverage (%)	Total number	bp	Total number of mapped contigs	Sequencing depth (fold)	Total of SNPs
1	45,064,769	36,886,997	81.9	21,887,208	719,138,056	63,889	16.6	10,980
2	36,823,111	31,152,504	84.6	19,972,645	656,243,813	53,822	18.3	4,113
3	37,257,345	32,175,988	86.4	19,309,856	634,463,329	51,236	17.5	2,773
4	35,863,200	27,331,878	76.2	15,718,358	516,454,041	69,662	14.6	9,891
5	30,039,014	24,458,877	81.4	14,277,427	469,092,491	51,892	15.7	1,032
6	32,124,789	25,763,900	80.2	14,992,102	492,566,411	53,317	15.8	1,165
7	30,357,780	24,230,102	79.8	13,935,933	457,866,127	55,090	15.4	7,561
8	28,530,027	22,970,652	80.5	13,106,335	430,601,662	53,667	15.2	6,426
9	23,843,360	19,060,074	79.9	11,008,304	361,678,832	41,137	15.7	178
10	23,661,561	18,592,212	78.6	10,572,960	347,371,203	43,569	15.3	3,617
11	30,828,668	22,439,806	72.8	12,582,930	413,402,408	58,282	14.5	12,216
12	27,757,321	21,114,982	76.1	11,932,390	392,027,726	58,990	14.1	7,099
Total or average^c	382,150,945	306,177,972	80.1^d	179,296,448	5,890,906,099	654,543	15.7	67,051

^a IRGSP, pseudomolecule build4
^bTotal length of aligned base except for unidentified base 'N'.
^cTotal number except the column of coverage and sequencing depth, these are discribed as average value.
^dCoverage is calcurated based on Koshihikari aligned length/Pseudomolecule of Nipponbare. The value is slightly different from average of coverage of respective chromosome.

ISSN: 1471-2164