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

Rice

Table 2 Statistics of mapping results by BWA

Data-set	Read type	Number of pre-processed reads	Uniquely mapped^a	Uniquely & properly mapped^b	Multiple^c	Unmapped^d
NIAS	SE, 36bp	59,344,842	38,193,181 (64.4%)	-	18,463,375 (31.1%)	302,057 (0.5%)
			[40,579,410 (68.4%)]^e
	SE, 51bp	50,981,527	34,124,172 (66.9%)	-	14,613,663 (28.7%)	385,876 (0.8%)
			[35,981,988 (70.6%)]
CSHL	PE, 76bp	246,779,548	191,891,774 (77.8%)	185,630,272 (75.2%)	40,901,655 (16.6%)	13,986,119 (5.7%)
				[190,608,407 (77.2%)]
	Unpaired PE^f, 76bp	10,316,471	7,235,730 (70.1%)	-	1,909,048 (18.5%)	819,735 (7.9%)
			[7,587,688 (73.5%)]

^a Number of uniquely mapped reads on the assembled pseudomolecules.
^b Number of uniquely mapped reads with proper distances between paired end reads.
^c Number of reads that mapped to multiple positions on the assembled pseudomolecules with the same score.
^d Number of reads that could not be mapped to the assembled pseudomolecules.
^e The numbers of reads in the square brackets includes mapped reads with lower mapping quality (MAPQ <20).
^f Unpaired reads for which one of the pair was discarded in the preprocessing and thus was mapped as a single-end read.