<p>This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.</p>
<p>On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.</p>

CC BY-SA 4.0
2020-08-21T07:28:43.197Z
Ok, I see. Thank you very much for your answer. QC was not performed, going to do this now.
snowflake
CC BY-SA 4.0
2020-09-19T15:05:30.100Z
Follow up question:https://bioinformatics.stackexchange.com/questions/14398/interpreting-gwas-results-with-different-settings
snowflake
CC BY-SA 4.0
2020-08-21T07:21:06.680Z
2020-08-21T07:21:06.680Z
winni2k
<p>I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).</p>
<p><a href="https://i.sstatic.net/w9x4I.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/w9x4I.png" alt="enter image description here" /></a></p>
<p>If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:</p>
<p><a href="https://i.sstatic.net/4tMdD.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/4tMdD.png" alt="enter image description here" /></a></p>
<p>Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.</p>
<p>How to interpret the dots in  a line?</p>

CC BY-SA 4.0
2020-08-21T06:33:39.750Z
I updated my question.
snowflake
CC BY-SA 4.0
2020-08-21T06:44:11.467Z
Thanks. How many samples and what organism? I assume this is a snp chip?
winni2k
CC BY-SA 4.0
2020-08-21T07:04:26.257Z
Barley with 200 phenotypes.
snowflake
CC BY-SA 4.0
2020-08-21T07:23:42.603Z
There seems to be something wrong with the Manhattan plots: snps from different chromosomes are overlapping? For example, green does can be found inside the region for red dots.
winni2k
<python><gwas>
GWAS MAC filter Interpretation
# GWAS MAC filter Interpretation

(Asked by: username_0 on 2020-08-19)

I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~ 3.8 which shows a strange pattern (many dots in one line with same value).

[![enter image description here](https://i.sstatic.net/w9x4I.png)](https://i.sstatic.net/w9x4I.png)

If I increase the filter to 6 % the dots in a line disappear but I loose also some significant SNPs:

[![enter image description here](https://i.sstatic.net/4tMdD.png)](https://i.sstatic.net/4tMdD.png)

Sample are about 77000 SNP positions (barley), unimputed from GWAS (all NaNs removed). GWAS was performed with 200 phenotype samples.

How to interpret the dots in a line?

**Tags:** python, gwas
> **Comments:**
> **username_0**: I updated my question.  
> **username_1**: Thanks. How many samples and what organism? I assume this is a snp chip?  
> **username_0**: Barley with 200 phenotypes.  
> **username_1**: There seems to be something wrong with the Manhattan plots: snps from different chromosomes are overlapping? For example, green does can be found inside the region for red dots.  

---

## 1 answers

### Answer by username_1 on 2020-08-21. Score: 1 | Accepted answer

This looks like genotyping failed for some samples. It's unclear from the op whether the genotyping data was controlled for quality, but I would recommend performing sample QC.

On a side note: in human gwas with imputed snps, I would expect to see clusters of significant snps as a sign that the significant snps are not an artifact. In the op there are some single significant snps. This might be a sign that those significant snps are artifacts. There are also some snps that form clusters and therefore look more promising.

> **Comments:**
> **username_0**: Ok, I see. Thank you very much for your answer. QC was not performed, going to do this now.  
> **username_0**: Follow up question:https://bioinformatics.stackexchange.com/questions/14398/interpreting-gwas-results-with-different-settings  

---

