# Typically what proportion of SNPs don't pass QC?
**URL:** https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782
**Category:** Day 2
**Created:** [June 3, 2026, 7:58pm UTC](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782 "2026-06-03T19:58:04Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)
#### Post date: [June 3, 2026, 7:58pm UTC](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782/1 "2026-06-03T19:58:04Z")
typically what proportion of SNPs don’t pass QC?
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### Author:  [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)
#### Post date: [June 3, 2026, 7:58pm UTC](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782/2 "2026-06-03T19:58:12Z")
It depends heavily on your dataset. In older datasets, it’s common to see higher percents. In newer datasets, percents will be lower.
The exception is excluding rare variants. Those haven’t actually “failed” quality control, they may just be too rare to use for your sample size and study design. So you exclude them during QC, but there isn’t actually something wrong with them, nothing failed during genotyping. Newer datasets will tend to have more SNPs excluded for that reason, because newer genotyping technologies can capture more rare variants.
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### Author:  [@anonymous](https://isgw-forum.colorado.edu/u/anonymous)
#### Post date: [June 3, 2026, 7:58pm UTC](https://isgw-forum.colorado.edu/t/typically-what-proportion-of-snps-dont-pass-qc/782/3 "2026-06-03T19:58:26Z")
we can impute back SNPs we drop so we prefer to drop SNPs not people