The indel event that can be seen between cusC and cusF between the native (IAI1) and heterologous (K12) genomes causes reads that align to the gapped area that slightly overlap cusC to be counted as expression for the cusC gene, causing a log-fold change in expression between the true and false expression levels of approximately 3.4, a highly significant difference.
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The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies.
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