Sentence examples for mapping quality were from inspiring English sources

Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used.

The parameters to control the mapping quality were: -k 1 –best –v 3. The alignment results were saved in SAM format files.

In all cases sequences with more than 50% ambiguously called bases (Ns) due to low read coverage or low mapping quality were discarded.

To avoid the effects of potential PCR duplicates, if multiple reads were aligned to the same position, all of the reads except for those with the highest mapping quality were removed using SAMtools (version 0.1.18, [ 45]) with the command 'samtools rmdup -s'.

CuReSim and CuReSimEval, a script that can be used to evaluate mapping quality, were developed in Java to run on all operating systems (see Section 2 of Additional file 1 for more details) and are freely available at http://www.pegase-biosciences.com/tools/curesim/.

In any case where there are two or more equally likely alignments (multiple locations a query can map to), the mapping quality is zero.

Average mapping quality was 30.

The mapping quality was assessed with SAMStat software [ 41].

Read mapping quality was assessed using Samtools v 0.1.19 [ 50].

For MaxSSmap we consider the read mapped only if mapping quality is above −100 log2.9=15.2.

The consensus mapping quality was also used to weed out low-quality assemblies.