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To detect potential errors in read mapping we assumed that selfing genotypes were largely homozygous, and therefore the presence of heterozygous sites in multiple selfing genotypes may indicate errors in read mapping (see Discussion).
To detect potential errors in read mapping we assumed that selfing genotypes were largely homozygous, and therefore the presence of the same heterozygous sites in multiple selfing genotypes would indicate errors in read mapping, possibly due to paralogous sequences.
A SHORE consensus analysis (Ossowski et al. 2008) was performed to obtain GC content and errors in read positions.
However, the Bayesian probabilistic model could not remove the large number of false positives caused by systematic errors in read alignment and base calling.
Reads mapped with mapping quality greater than or equal to 10 and bases with base quality greater than or equal to 17 were used for variant calling to avoid false positives due to errors in read alignment and sequencing errors.
Assuming that selfing genotypes are largely homozygous, the presence of heterozygous sites in multiple samples of selfers may indicate errors in read mapping (see Discussion).
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