Table 2 Fixed genomic differences between bulked F2 individuals of pep1-1 and fde1

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   De novo annotationb   Agreement of annotations
pep1-1 fde1 Mutant genome Length (bp) Mutation position Mirror countc Homolog Chr. Positiond Effect
T C pep1-1 549 437 0 2 5,482,633 Intergenic   None   Yes
T C pep1-1 625 236 0 AT5G08160 5 2,627,760 Syn. (L > L)   Syn. (L > L)   Yes
T C pep1-1 807 410 0 AT5G08510 5 2,754,082 Intronic   Intronic   Yes
A G pep1-1 829 354 0 AT5G09670 5 2,998,250 Exonic   None   No
A G pep1-1 889 408 0 AT5G10140 5 3,175,363 Splice-site change   Splice-site change   Yes
T C pep1-1 812 451 0 5 3,219,708 Intergenic   None   Yes
T C pep1-1 653 220 17 AT5G10550 5 3,333,724 Syn. (R > R)   Syn. (R > R)   Yes
A G pep1-1 783 437 0 5 3,336,193 Intergenic   None   Yes
T C pep1-1 780 348 26 AT5G11850 5 3,818,093 Nonsyn. (G > D)   Nonsyn. (G > D)   Yes
A G pep1-1 882 445 29 5 10,116,108 Intergenic   Nonsyn. (F > S)   No
A G pep1-1 732 368 0 AT5G44050 5 17,725,725 Intronic   Intronic   Yes
A G pep1-1 772 341 21   None   NA
A G pep1-1 850 448 0   Nonsyn. (E > K)   NA
G A fde1 828 410 0 AT4G34320 4 16,422,853 Nonsyn. (Q > STOP)   Nonsyn. (Q > STOP)   Yes
G A fde1 745 361 0 AT4G35230 4 16,756,818 Intronic   Intronic   Yes
G A fde1 637 261 0 4 17,051,245 Intergenic   None   Yes
G A fde1 806 388 0 4 17,135,887 Intergenic   None   Yes
C T fde1 819 388 1 AT4G36360 4 17,178,292 Nonsyn. (G > E)   Nonsyn. (G > E)   Yes
C T fde1 863 427 0 AT4G36660 4 17,286,500 Intronic   Nonsyn. (E > K)   No
C T fde1 764 313 10 4 17,357,762 Intergenic   None   Yes
C T fde1 880 454 0 AT4G36920 4 17,401,794 Nonsyn (D > N)   Nonsyn (D > N)   Yes
G A fde1 798 385 4 4 17,460,182 Intergenic   None   Yes
C T fde1 789 353 0 AT4G37080 4 17,475,571 Nonsyn. (A > T)   Nonsyn. (A > T)   Yes
G A fde1 863 429 0 4 17,729,980 Intergenic   None   Yes
G A fde1 745 381 0   None   NA
C T fde1 903 476 0   None   NA
G A fde1 503 79 0   None   NA
G A fde1 630 254 0   None   NA
G A fde1 922 455 30   None   NA
  1. Chr., chromosome identifier; syn., synonymous base substitution; nonsyn., nonsynonymous base substitution; NA, not applicable.
  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. bDe novo gene annotation was performed on the contigs using Augustus annotation tool, mutations were annotated after their effect on this gene structure.
  4. cMirror 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 fractions of wild-type alleles and can be used for prioritizing mutations.
  5. dMarked positions indicate contig alignments for which only regions flanking the mutation mapped to A. thaliana. Hence, these inferred positions are estimates.