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Indeed, we performed a cursory analysis for TE/repeat contents in regions that were identified as being deletions relative to the reference sample.
When such areas consist of three or more consecutive SNP-bearing reads covered by six or more reads, these are defined as being deletions.
Many of the CNV calls we see for these mice (30 175 calls with the majority of events being deletions) could errantly arise from their genomic DNA failing to hybridize strongly to a number of probe sets in a genomic region because they have diverged from the C57BL/6 J mice in those regions, i.e. have undergone multiple base substitutions or mutations, rather than copy number changes.
We observed that all accessions had similar results among the DNA polymorphisms with 88.7% being substitutions, 4.5% being insertions, and 6.6% being deletions (Figure 1b).
Similar(56)
The vast majority were deletions and translocations distributed across the genome (Extended Data Fig. 4c).
About 7% of mutations in MTM1 are deletions.
Four of them were deletions and another four are duplications.
Three were insertions, indicating that additional nucleotides should be inserted into the reference genome, while the other two were deletions.
Since BWA generates gapped alignments, small insertion/deletion (indel) type variants (1 4 bp gaps) could also be detected: 642 sites were insertions and 797 were deletions.
Interestingly, 12 of these 13 CNVs were deletions.
In all, 41.9% of all EGFR mutations were deletions, 39% were substitutions and 19.5% were complex deletion-insertions (delins).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com