---
name: "sam-stats"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sam-stats"
---

# sam-stats(1)

ea-utils: produce digested statistics

## NAME

sam-stats - ea-utils: produce digested statistics

## SYNOPSIS

**sam-stats** \[*options*\] \[*file1*\] \[*file2*...*filen*\]

## DESCRIPTION

Version: 1.38.681

Produces lots of easily digested statistics for the files listed

Options (default in parens):

**-D**             Keep track of multiple alignments **-O** PREFIX      Output prefix enabling extended output (see below) **-R** FIL         Coverage/RNA output (coverage, 3' bias, etc, implies **-A**) **-A**             Report all chr sigs, even if there are more than 1000 **-b** INT         Number of reads to sample for per-base stats (1M) **-S** INT         Size of ascii-signature (30) **-x** FIL         File extension for handling multiple files (stats) **-M**             Only overwrite if newer (requires **-x**, or multiple files) **-B**             Input is bam, don't bother looking at magic **-z**             Don't fail when zero entries in sam

OUTPUT:

If one file is specified, then the output is to standard out.  If multiple files are specified, or if the **-x** option is supplied, the output file is \<filename\>.\<ext\>.  Default extension is 'stats'.

Complete Stats:

- \<STATS\>

  : mean, max, stdev, median, Q1 (25 percentile), Q3

- reads

  : # of entries in the sam file, might not be # reads

- phred

  : phred scale used

- bsize

  : # reads used for qual stats

- mapped reads

  : number of aligned reads (unique probe id sequences)

- mapped bases

  : total of the lengths of the aligned reads

- forward

  : number of forward-aligned reads

- reverse

  : number of reverse-aligned reads

- snp rate

  : mismatched bases / total bases (snv rate)

- ins rate

  : insert bases / total bases

- del rate

  : deleted bases / total bases

- pct mismatch

  : percent of reads that have mismatches

- pct align

  : percent of reads that aligned

- len \<STATS\>

  : read length stats, ignored if fixed-length

- mapq \<STATS\>

  : stats for mapping qualities

- insert \<STATS\>

  : stats for insert sizes

- %\<CHR\>

  : percentage of mapped bases per chr, followed by a signature

### Subsampled stats (1M reads max):

-

  base qual \<STATS\> : stats for base qualities %A,%T,%C,%G       : base percentages

### Meaning of the per-chromosome signature:

-

  A ascii-histogram of mapped reads by chromosome position. It is only output if the original SAM/BAM has a header. The values are the log2 of the # of mapped reads at each position + ascii '0'.

### Extended output mode produces a set of files:

- .stats

  : primary output

- .fastx

  : fastx-toolkit compatible output

- .rcov

  : per-reference counts & coverage

- .xdist

  : mismatch distribution

- .ldist

  : length distribution (if applicable)

- .mqdist

  : mapping quality distribution