Question: why Samtools Flagstat Results showing very less reads mapped
gravatar for inayat45shaikh
6.2 years ago by
inayat45shaikh40 wrote:

Hello group,

i am trying to get the percentage of reads mapped to refernce using samtools. i used the command samtools flagstat sequence.bam , but the result i am getting is bit worst than i was expecting, as it shows only 34% of reads mapped.

438974667 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
151842378 + 0 mapped (34.59%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

i wanted to know why i am getting this result, and where have i done mistake and how can fix this problem.

Thanks in advance


next-gen • 1.9k views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 6.2 years ago by inayat45shaikh40

I need to know more to be able to answer that -

What program did you use for alignments? Which settings, what insert size did you use? How complete is your reference? Is it the same species, or are you using a different reference genome? Is it mate-paired data? Did you have a look at the quality of your reads using FastQC?

ADD REPLYlink modified 7 months ago by RamRS28k • written 6.2 years ago by Philipp Bayer6.7k

Hi Philipp,

i have a single-end data and i want to map this to its assembled contigs to assess assembly quality and calling variants. i used BWA for alignment.

ADD REPLYlink written 6.2 years ago by inayat45shaikh40

How well reads will map to assembled contigs will depend entirely on the quality of the assembly. My guess is that this assembly is a bit lacking.

ADD REPLYlink written 6.2 years ago by Devon Ryan96k
gravatar for Devon Ryan
6.2 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

The results that it shows are simply the metrics that exist. If you want a higher alignment rate, then perhaps tweaking the aligner settings or changing how reads are pre-processed would be useful. Samtools just reports what's in the BAM file, nothing more.

ADD COMMENTlink written 6.2 years ago by Devon Ryan96k
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