the query sequence for this alignment, SEQ.length of this group from the leftmost position to the rightmost position, ISIZE or TLEN.Beware to always use the correct base when referencing positions. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. leftmost position of where the next alignment in this group maps to the reference, MPOS or PNEXT.(A group is alignments with the same query name.) In paired alignments, it is the mate's reference sequence name. the reference sequence name of the next alignment in this group, MRNM or RNEXT.string indicating alignment information that allows the storing of clipped, CIGAR.mapping quality, MAPQ, which contains the "phred-scaled posterior probability that the mapping position" is wrong.leftmost position of where this alignment maps to the reference, POS.reference sequence name, RNAME, often contains the Chromosome name.Not all alignments contain The rest of the alignment fields may be set to default values if the information is unknown. is this read a PCR or optical duplicate?.is the next fragment the reverse strand?.a bitwise set of information describing the alignment, FLAG.It is used to group/identify alignments that are together, like paired alignments or a read that appears in multiple alignments. query name, QNAME (SAM)/read_name (BAM).What Information Does SAM/BAM Have for an Alignment The alignment section contains the information for each sequence about where/how it aligns to the reference genome. The alignments then associate themselves with specific header information. The header section may contain information about the entire file and additional information for alignments. Refer to the specs to see a format description.īoth SAM & BAM files contain an optional header section followed by the alignment section. SAM files and BAM files contain the same information, but in a different format. If you are writing software to read SAM or BAM data, our C++ libStatGen is a good resource to use. The current definition of the format is at. In the future, SAM will also be used to archive unaligned sequence data generated directly from sequencing machines. Most often it is generated as a human readable version of its sister BAM format, which stores the same data in a compressed, indexed, binary form.Ĭurrently, most SAM format data is output from aligners that read FASTQ files and assign the sequences to a position with respect to a known reference genome. The SAM Format is a text format for storing sequence data in a series of tab delimited ASCII columns. 2.2 What Information is in the SAM/BAM Header.2.1 What Information Does SAM/BAM Have for an Alignment.
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