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Table 2 Statistics of mapping results by BWA

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

Data-set Read type Number of pre-processed reads Uniquely mappeda Uniquely & properly mappedb Multiplec Unmappedd
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 PEf, 76bp 10,316,471 7,235,730 (70.1%) - 1,909,048 (18.5%) 819,735 (7.9%)
    [7,587,688 (73.5%)]    
  1. a Number of uniquely mapped reads on the assembled pseudomolecules.
  2. b Number of uniquely mapped reads with proper distances between paired end reads.
  3. c Number of reads that mapped to multiple positions on the assembled pseudomolecules with the same score.
  4. d Number of reads that could not be mapped to the assembled pseudomolecules.
  5. e The numbers of reads in the square brackets includes mapped reads with lower mapping quality (MAPQ <20).
  6. f Unpaired reads for which one of the pair was discarded in the preprocessing and thus was mapped as a single-end read.