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Samtools Pileup Characters

I know $ means end of read and ^ beginning of read, wikipedia says that:

+[0-9]+[ACGTNacgtn]+ denotes an insertion of one or more bases

-[0-9]+[ACGTNacgtn]+ denotes a deletion of one or more bases

So what does caret followed by a closed bracket mean?

gg$GGGgGggG^]G

samtools mpileup
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updated by Andreas Andreas • written by axelwilhelm axelwilhelm

1 answer

Six G's on the reverse strand (lower case), Six G's on the forward strand (uppercase), once the end of a read (the dollar sign) one start of a read segment (the caret sign) followed by the "ASCII of the character following ^ minus 33 gives the mapping quality" which is in this case: ord(']')-33=60 See the pileup format description

Andreas

Note: Corrected an earlier version which wrongly used ord('[')-33=58.

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written by Andreas Andreas

Exactly, thanx for reminding. ]-33=60.

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written by axelwilhelm axelwilhelm

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