Sentence examples for mapping quality less from inspiring English sources

Reads with mapping quality less than 30, and duplicate reads were discarded using samtools.

Reads with mapping quality less than 30, and reads mapped to the mitochondria genome or the hg19 consensus excludable region (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) were filtered out.

For each deeply sequenced sample, low-quality alignments (mapping quality less than 1, unmapped, duplicates, and non-unique) were filtered using BamTools [ 37].

We ignore reads with mapping quality less than 30 and we ignore bases whose quality score is less than 30; quality score of 30 represents 1/1000 probability of error.

The DTN measure for a given read along with the host and transgene mapping quality scores are used to remove PCR duplicates (all reads with DTN = 0) and poor quality reads (reads with mapping quality less than 20).

We identified regions of low-coverage using criteria defined by the Sanger sequencing project, specifically mapping quality less than 40 (PHRED scale) or coverage depth greater than 150 (indicating duplication) [ 5].

Positions with root mean squared mapping qualities less than 15 and insertion/deletion polymorphisms were ignored.

Sequence reads with mapping quality scores less than 20 were ignored in variant selection.

The recalibrated BAM files were filtered by removing all reads with mapping quality Phred score [ 28] less than 20 and all bases with base quality Phred score less than 20 (meaning that the probability of the base call being wrong is less than 0.01).

We also analyzed breed specificity for 280 putative deletions that resulted from applying a less stringent read mapping quality constraint, which was also applied in previous SV detection studies [ 19, 25].

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.