Table utilities / SAM flag decoder
Your data stays in your browser: files are read and processed on your device, never uploaded to any server, and cleared when you close the page. Free, no sign-in.
The flag in column 2 of SAM/BAM is the sum of 12 binary bits, each marking a state (paired, properly paired, unmapped, reverse strand, read 1/2, secondary, duplicate, supplementary, etc.). The table splits each flag into its bits with plain-language meanings and a category.
Common values: 99/147 and 83/163 are properly paired reads (read 1 forward/read 2 reverse, and read 1 reverse/read 2 forward); 77/141 are pairs with both reads unmapped; 256 marks secondary and 2048 supplementary alignments (chimeric reads or reads spanning structural variants).
When you paste a whole SAM file or a count table, the summary gives the mapping, proper-pair and duplicate rates of primary alignments (as in samtools flagstat, excluding secondary and supplementary records).
Tick the bits below to encode a flag value, e.g. for samtools view -f / -F filters.
Sequence Alignment/Map Format Specification v1.6, section 1.4; Li et al. 2009 (Bioinformatics 25:2078).
When pasting SAM records, up to about one million lines is recommended; for large files count flags with samtools first.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.