Sentence examples for had mapping quality from inspiring English sources

Only reads that mapped uniquely to a single reference sequence and had mapping quality ≥ 37 were included in subsequent analyses.

Approximately 86.16% and 86.14% of the reads in the H and L groups had mapping quality ≥ 20, respectively.

Reads that mapped to multiple locations equally well according to MAQ's quality-aware alignment algorithm (i.e. had mapping quality scores of 0) were discarded.

Second, variants were not forwarded to the next step if (i) more than 5% of reads had mapping quality 0, (ii) coverage was more than six fold higher compared to the mean coverage, or (iii) a SNP quality score was below 100.

Default settings were used (minimum read mapping/base quality to consider a read/base for variant calling 10; ≥ 1 read supporting variant must have mapping quality ≥ 20; ≥ 4 reads per pool; contingency table threshold p = 10-3; quality values based p-value threshold 10-5).

Read mappings were retained if they met the following criteria: they had a mapping quality of 99, or had no mismatches, or the sum of the quality scores of the mismatched bases was less than or equal to six (using Phred quality scores).

For non-coding sites 4% could be explained by missed indels, 93% were in reads that had low mapping quality scores and/or were orphan pairs, suggesting that the read could have been misaligned, and 3% appeared truly homozygous.

Out of 240 coding sites examined, 53% were caused by indels that were too large for maq to properly align the reads, 36% were in reads that had low mapping quality scores and/or were orphan pairs, suggesting that the read could have been misaligned, 9% appeared truly homozygous, and 2% could not be explained.

These reads may have lower mapping quality or have been clipped.

For these datasets, we retained bi-allelic SNPs that were not near a high-quality indel (i.e., did not receive a BCFTools code of "G" in any dataset), had a mapping quality score > 40 in at least one dataset, and probabilities < 10-2, 10-3, or 10-4 in at least one dataset.

The majority of reads (>80%) had a mapping quality score ≥30.