Sentence examples for mapping quality lower from inspiring English sources

We removed reads generated from polymerase chain reaction duplicates with Picard v1.96, and reads with mapping quality lower than 30 were excluded for further analysis.

For this, SNP calls were further filtered ignoring: 1) bases with quality lower than 20, 2) bases in reads with mapping quality lower than 15, and 3) positions with less than 20 reads mapped.

For the SNV calling, the reads with a mapping quality lower than 15 are not considered.

We first discarded alignments with the mapping quality lower than 30, and then made variant calls by mpileup and bcftools programs embedded in SAMtools [ 20].

Next we filtered out read alignments with a mapping quality lower than 30, which avoids reads mapped to multiple locations alignments with low similarity.

SNPs were called using the haplotype caller module and raw variants were filtered using GATK's variant quality score recalibration selecting sites with a minimum raw coverage of 10, Root Mean Square mapping quality lower than 40, quality by depth greater than 2 and haplotype score greater than 13.

Mapping quality of 454 dataset was lower that the ones of the other two: mean and median mapping were both about 54%, and less than 3% had mapping above 95%.

This difference is unlikely to be due to divergence from the reference because we observed no systematic differences in mapping quality metrics between the European- and Bantu- admixed Family 1 and the KhoeSan Family 2. Due to lower mapping rates, SA006 and SA035 displayed overall lower mapped coverage than the other samples.

Reads with mapping quality zero were discarded.

MAQ and BWA generate mapping qualities.

Reads were mapped to the revised Cambridge reference sequence (GenBank ID NC_012920, the starting point was changed to 15978 on the original sequence) using BWA [ 56]; reads with mapping quality score lower than 20 and bases with quality score lower than 20 were excluded from the analysis, resulting in a final average coverage of 49334-fold per position in the target region.