Therefore, the mapping efficiency bias was unlikely to explain the large number of the freshwater-increased GCNVs.
PolyCat uses GSNAP's single-nucleotide polymorphism (SNP -tolerant mapping to minimize the mapping efficiency biaSNP -tolerantNPs between genomapping
These "homoeo-SNPs" can be used to reduce mapping efficiency bias through the use of SNP-tolerant mapping, as with heterozygous genes in humans (Wu and Nacu 2010).
To examine whether the detected GCNVs were derived from the mapping efficiency bias toward the freshwater group, we investigated the frequencies of SNVs of the 19 freshwater-increased GCNVs using reads that were mapped with the '-e 100' option.
To test for such a bias in mapping efficiency, we applied our read mapping procedure to simulated RNA-seq reads from each population.
The SNP index and read categorization process facilitated the analysis of allopolyploid cotton by reducing the bias in mapping efficiency between the two genomes and by providing a means to separate data generated for each allopolyploid genome (AT- and DT-genomes in cotton).
Additional factors, however, such as PCR amplification bias and differential mapping efficiency could potentially impact coverage, complicating quantitative interpretation of insertion site sequencing data.
To exclude bias due to intragenomic variation in mapping efficiency, the number of average sequence reads was normalized to the number of sequence reads obtained from control (input) samples to which MBD protein was not applied.
Reduced gene body methylation in Cvi is unlikely to be a technical artifact of mapping biases: gene bodies have fewer SNPs and indels than TEs and thus mapping efficiency is better to genes than to TEs.
The effect of indels on the mapping efficiency strongly depends on the mapping software.
