Table 2 SAMQA Biological Tests
From: SAMQA: error classification and validation of high-throughput sequenced read data
Biological Tests | Inclusion Criteria |
|---|---|
Mapping quality | Low Phred-adjusted mapping quality score |
Read length | Shortened read lengths for a given sequencing technology |
Read count | Low aggregate number of reads for a given sequencing technology |
Read frequency | Low number of reads for a given set of kilobase regions |
Coverage | Low coverage for a given read group, chromosome, or kilobase region |
Structural variations | High numbers of localized structural variation |
Anomalous sequence data | Instances of "random" chromosomes from human assembly [8] |
Population estimates of structural variation | Very high projected structural variation across different platform units |
Read group correlation | Low mapping quality correlation for megabase regions, across read groups Low coverage correlation of megabase regions, across read groups |