Table 2.
SNPs called from contaminating human reads within publicly archived bacterial sequencing datasets
|
Status of sample |
No. of samples |
% of samples |
|---|---|---|
|
Contains one or more human SNPs |
7389 |
63.8 |
|
Contains one or more human SNPs with ≥2 reads supporting alternative allele, QUAL ≥ 20, and MAPQ = 60 |
1657 |
14.3 |
|
Contains one or more human SNPs considered ‘common’ in dbSNP |
5113 |
44.1 |
|
Contains one or more ‘common’ human SNPs, each with ≥2 reads supporting alternative allele, QUAL ≥ 20, and MAPQ = 60 |
731 |
6.3 |
|
Contains one or more human SNPs recorded in ClinVar |
412 |
3.6 |
|
Contains one or more human SNPs recorded in ClinVar, each with ≥2 reads supporting alternative allele, QUAL ≥ 20, and MAPQ = 60 |
191 |
1.6 |
|
Contains one or more ‘common’ human SNPs recorded in ClinVar, each with ≥2 reads supporting alt allele, QUAL ≥ 20, and MAPQ = 60 |
13 |
0.11 |