How to understand SAM flag

#BinaryDecimalHexadecimalDescription
1110x1Read paired
21020x2Read mapped in proper pair
310040x4Read unmapped
4100080x8Mate unmapped
510000160x10Read reverse strand
6100000320x20Mate reverse strand
71000000640x40First in pair
8100000001280x80Second in pair
91000000002560x100Not primary alignment
1010000000005120x200Read fails platform/vendor quality checks
111000000000010240x400Read is PCR or optical duplicate
1210000000000020480x800Supplementary alignment

Instruction
: enter whatever SAM flag (e.g. 99) to get a quick interpretation of its meaning, or click on arbitrary rows to select/deselect them to calculate the corresponding flag value. As you can see, your typed flag is a just sum of the matched bits in green.


http://www.samformat.info/sam-format-flag



Comments

Popular posts from this blog

gspread error:gspread.exceptions.SpreadsheetNotFound

Miniconda installation problem: concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

转载:彻底搞清楚promoter, exon, intron, and UTR