Table 3 Genes with independent lesions in pep1-1 and pep1-2

From: Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

Allele Contig assoc. with mutation Homology-based annotationa
pep1-1 fde1 Mutant genome Length (bp) Mutation position Mirror countb Homolog Chr. Position Effect
T C pep1-2 404 261 0 AT2G24680 2 10,495,120 Intronic
C T pep1-1 640 267 0 AT2G24680 2 10,496,039 Intronic
A G pep1-1 552 280 0 AT4G11670 4 7,048,540 Intronic
G A pep1-2 441 161 0 AT4G11670 4 7,050,257 Intronic
T C pep1-1 532 267 0 AT5G10140 5 3,175,363 Splice-site change
C T pep1-2 660 320 0 AT5G10140 5 3,175,642 Nonsyn. (R > STOP)
  1. Chr., chromosome identifier; nonsyn., nonsynonymous base substitution.
  2. aContigs were aligned against NCBI Genomic Reference Sequences. All contigs that had a reliable hit against one of the genomes also featured a reliable hit against A. thaliana. For uniformity we report only the hits against the A. thaliana reference sequence.
  3. bMirror count describes the number of wild-type k-mers that were identified within the mutant samples while generating the respective seed. It indicates the presence of low fraction of wild-type alleles and can be used for prioritizing mutations.