![]() The formula to calculate the \(MAPQ\) value is: \(MAPQ=-10*log10(p)\), where \(p\) is the probability that the read is mapped wrongly. It seems a reasonable idea to only keep good mapping reads.Īs the SAM-format contains at column 5 the \(MAPQ\) value, which we established earlier is the “MAPping Quality” in Phred-scaled, this seems easily achieved. In this section we want to sub-select reads based on the quality of the mapping. One line of a mapped read can be seen here: ![]() Variable OPTional fields in the format TAG:VTYPE:VALUE Query QUALity (ASCII-33 gives the Phred base quality) Query SEQuence on the same strand as the reference Mate Reference sequence NaMe (‘=’ if same as RNAME) ¶ġ-based leftmost POSition/coordinate of clipped sequence ![]() The columns of such a line in the mapping file are described in Table 5.1. Then, for each read, that mapped to the reference, there is one line. Have a look into the sam-file that was created by either program.Ī quick overview of the sam-format can be found here and even more information can be found here.īriefly, first there are a lot of header lines. BWA, like most mappers, will produce a mapping file in sam-format. ![]()
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