Open SAM files in your browser
Where each read of a sequencing run landed on the genome, as aligners write it. Open a SAM right here as a row for each read. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your alignments open as a row for each read, the first rows on show while the rest are read.
- A row for each read • Position, CIGAR, mate and tags
- Sort and filter • Counts for every column
- Flags in words • References, read groups and programs
- Export • Save as CSV, Excel, JSON or Parquet
About SAM
Heng Li and the 1000 Genomes Project made SAM in 2009 with SAMtools, and aligners like BWA, Bowtie 2, minimap2 and STAR write it. Its binary twin, BAM, is how alignments are usually kept, and samtools view turns one into the other.
A SAM starts with header lines that begin with @: the reference sequences and their lengths, read groups and the programs that made it. Then each line is a read in eleven fields, its name, a flag, the reference and position it maps to, its mapping quality, a CIGAR of how it lines up, its mate's place, its letters and its qualities, followed by tags like NM:i:1.
Filepeek reads the file in pieces in your browser and shows each read as a row, its flag spelled out in words, like forward, paired, proper pair, to sort, search and filter like any table. Show details lists the references, read groups, samples and programs, and Export saves the rows as CSV, Excel, JSON or Parquet.
Sequence Alignment/Map
.sam
Format
- MIME type
- text/x-sam
- Made by
- Heng Li and the 1000 Genomes Project, for SAMtools
- Released
- 2009
Inside the file
- Header
- References, read groups and programs
- Each read
- Eleven fields split by tabs
- Then
- Tags like NM:i:1
- Binary twin
- BAM
Opens in every browser
Filepeek opens SAM files of any size in Chrome, Edge, Firefox and Safari, read in pieces so the first reads show at once. On their own, browsers download them or show them as text.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open SAM
- WindowsNo app built in reads it • IGV and samtools do
- MacNo app built in reads it • IGV and samtools do
- iPhone and iPadNo app opens it
- AndroidNo app opens it
Questions
What does a read's flag mean?
Each bit of the number says one thing: 1 paired, 2 proper pair, 4 unmapped, 16 reverse strand, 64 first and 128 second in its pair, 256 secondary, 1024 duplicate and 2048 supplementary. Filepeek spells each flag out in the Flags column, so 99 reads forward, paired, proper pair, mate reverse, first in pair.
How do I read a CIGAR?
It says how the read lines up with the reference, a count and a letter at a time: M letters that align, I letters inserted in the read, D letters deleted from it and S letters soft-clipped at its ends. So 45M2I53M is 100 letters with 2 inserted.
Why are some reads at position 0?
A read that didn't map has no place on the reference, so its position is 0 and its reference is *. Filter Flags for unmapped to find them.
Can I open a BAM file?
Yes. BAM, SAM's compressed binary twin, opens the same way, unpacked a block at a time.