<p>Yes, this is expected.</p>
<p>If a read maps equally well to two different locations in the reference database, then the minimum probability that read maps to another location is 0.5. MAPQ scores are ten times the negative <code>log10</code> of the <a href="https://www.acgt.me/blog/2014/12/16/understanding-mapq-scores-in-sam-files-does-37-42" rel="nofollow noreferrer">probability of a mismatch</a>, so a mismatch probably of 0.5 would lead to a <em>maximum</em> MAPQ score of <span class="math-container">$-10*log_{10}(0.5) = 3$</span>. If there's any doubt about the mapping (e.g. a mismatch in the sequenced read), or the read could map to more than two locations, then that probability will drop further. I would not be surprised if these MAPQ scores, where the location is impossible to precisely determine, were rounded down to 0.</p>

CC BY-SA 4.0
2022-04-26T02:16:38.077Z
2022-04-26T02:16:38.077Z
gringer
<p>I have two very similar genomes in my bowtie2 database (nuc similarity &gt; 90 %). When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a MAPQ score of 0. Only at the positions that are different between the two genomes I get higher MAPQ scores.</p>
<p>I also created a database with just one of the genomes, inspecting the MAPQ score of a single read. This single read gets a MAPQ score of 24 when the database contains only one genome, but drops to zero when two similar genomes are in the database.</p>
<p>Is this the expected behavior?
My understanding of the MAPQ score computation is, that the alignment score of a read at a specific location is only compared to the score at other positions within the same reference, not across the whole database.
If the alignment scores for a read are then pretty close to each other, it is assumed that the read does not map uniquely, which is reflected in a low MAPQ score.</p>
<p>So my question is, whether the alignment score of a read is compared to other alignments of this read within the same reference OR against alignments with the whole database index?
Changing the database, would then result in different MAPQ scores.</p>

CC BY-SA 4.0
2022-04-25T16:46:42.210Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
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<bowtie2><mapq>
Is the Bowtie2 MAPQ score dependent on the database index?
# Is the Bowtie2 MAPQ score dependent on the database index?

(Asked by: username_0 on 2022-04-25)

I have two very similar genomes in my bowtie2 database (nuc similarity > 90 %). When mapping with bowtie2 against this database, most of the reads that are mapped to one of these genomes have a MAPQ score of 0. Only at the positions that are different between the two genomes I get higher MAPQ scores.

I also created a database with just one of the genomes, inspecting the MAPQ score of a single read. This single read gets a MAPQ score of 24 when the database contains only one genome, but drops to zero when two similar genomes are in the database.

Is this the expected behavior?
My understanding of the MAPQ score computation is, that the alignment score of a read at a specific location is only compared to the score at other positions within the same reference, not across the whole database.
If the alignment scores for a read are then pretty close to each other, it is assumed that the read does not map uniquely, which is reflected in a low MAPQ score.

So my question is, whether the alignment score of a read is compared to other alignments of this read within the same reference OR against alignments with the whole database index?
Changing the database, would then result in different MAPQ scores.

**Tags:** bowtie2, mapq
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  

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## 1 answers

### Answer by username_2 on 2022-04-26. Score: 0

Yes, this is expected.

If a read maps equally well to two different locations in the reference database, then the minimum probability that read maps to another location is 0.5. MAPQ scores are ten times the negative `log10` of the [probability of a mismatch](https://www.acgt.me/blog/2014/12/16/understanding-mapq-scores-in-sam-files-does-37-42), so a mismatch probably of 0.5 would lead to a *maximum* MAPQ score of $-10\*log\_{10}(0.5) = 3$. If there's any doubt about the mapping (e.g. a mismatch in the sequenced read), or the read could map to more than two locations, then that probability will drop further. I would not be surprised if these MAPQ scores, where the location is impossible to precisely determine, were rounded down to 0.


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