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* more README.md work
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README.md

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@@ -4,10 +4,11 @@ The official SAMtools repository can be found at: http://samtools.sourceforge.ne
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## Major fixes:
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- added "samtools sample" command, to sample reads from a SAM/BAM file at a given frequency.
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- added "samtools qa" command, to compute the mean and median coverage, as well a histogram
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from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX.
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Furthermore, "other" information is also available in the output file, namely:
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from 1 to N (defined by param) containing the number of bases covered a maximum of 1X, 2X...NX.
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Furthermore, "other" information is also available in the output file, namely:
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- Total number of reads
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- Total number of duplicates found and ignored (duplicates are "found" based on the sam flag and are ignored in the counting of coverage)
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- Total number of duplicates found and ignored (duplicates are "found" based on the sam flag
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and are ignored in the counting of coverage)
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- Percentage of unmapped reads
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- Percentage of zero quality mappings
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- Number of proper paired reads (based on sam flag of proper pairs)

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