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can you tell me please how to get the percentage of the coverage ?

Hello Biostar I hope you're doing well i mapped my reads against the reference genome to get an idea about the coverage , what i want to know is the percentage of the coverage , but i don't know how to obtain this information using the diffrent tools i know , in qualimap , i just found the mean coverage and std coverage data also lines like this

There is a 99.59% of reference with a coverageData >= 1X
     There is a 99.56% of reference with a coverageData >= 2X
     There is a 99.53% of reference with a coverageData >= 3X
     There is a 99.49% of reference with a coverageData >= 4X
     There is a 99.45% of reference with a coverageData >= 5X
     There is a 99.42% of reference with a coverageData >= 6X
     There is a 99.39% of reference with a coverageData >= 7X
     There is a 99.37% of reference with a coverageData >= 8X
     There is a 99.34% of reference with a coverageData >= 9X
     There is a 99.31% of reference with a coverageData >= 10X
     There is a 99.3% of reference with a coverageData >= 11X
     There is a 99.27% of reference with a coverageData >= 12X..

i don't know if it s possible to obtain the percentage of the coverage using this informations and how ,

Also i used bamtools stats , and obtained these informations

Total reads:       6158542
Mapped reads:      5749217 (93.3535%)
Forward strand:    3286294 (53.3616%)
Reverse strand:    2872248 (46.6384%)
Failed QC:         0 (0%)
Duplicates:        0 (0%)
Paired-end reads:  6158542 (100%)
'Proper-pairs':    4667096 (75.7825%)
Both pairs mapped: 5730384 (93.0477%)
Read 1:            3079271
Read 2:            3079271
Singletons:        18833 (0.305803%)

and the same thing i didn't get the percentage of coverage and the same thing with samtools flagstat

6158542 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
5749217 + 0 mapped (93.35% : N/A)
6158542 + 0 paired in sequencing
3079271 + 0 read1
3079271 + 0 read2
4667096 + 0 properly paired (75.78% : N/A)
5730384 + 0 with itself and mate mapped
18833 + 0 singletons (0.31% : N/A)
83794 + 0 with mate mapped to a different chr
12721 + 0 with mate mapped to a different chr (mapQ>=5)

and samtools idxstats

NZ_ALWU01000001.1 581415 2031429 6451
NZ_ALWU01000002.1 43553 76489 678
NZ_ALWU01000003.1 29286 117672 342
NZ_ALWU01000004.1 37537 144448 440
NZ_ALWU01000005.1 217837 789901 2467
NZ_ALWU01000006.1 38235 103338 325
NZ_ALWU01000007.1 9944 45471 292
NZ_ALWU01000008.1 178611 651422 2190
NZ_ALWU01000009.1 17047 6352 42
NZ_ALWU01000010.1 510276 1782695 5606
* 0 0 390492

can you tell me please how to get the percentage of the coverage ? Thank you very much

sequencing assembly next-gen
• 35 views • link
updated by GenoMax GenoMax • written by AbdelAbdel • AbdelAbdel 
$ samtools depth

Usage: samtools depth [options] in1.bam [in2.bam [...]]

The output is a simple tab-separated table with three columns: reference name,
position, and coverage depth.  Note that positions with zero coverage may be
omitted by default; see the -a option.

You could also use another program called mosdepth.

can you tell me please how to get the percentage of the coverage ?

The depends. At what level. Base pair, chromosome or genome?

• 0 views • link
written by GenoMax GenoMax

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