Table 1.
Perfect-match SE-50bp 20-fold genomes, mapping and genome coverage.
Table 2.
Percentage of uncovered sequence using various perfect-match data setsa.
Fig 1.
Sensitivity of variant-calling pipelines for EMS-type mutations.
The percentage of true-positive (TP) mutation calls is indicated for each combination of aligner plus variant caller (F, FreeBayes; G, GATK HaplotypeCaller; S, SAMtools/BCFtools; V, VarScan2) and plotted separately for different categories of variants. Homozyous (blue) and heterozygous (red) mutation calls are indicated by color. Asterisks (*) indicate the best-performing pipelines in each category. (A) Homozygous SNPs. (B) Heterozygous SNPs. (C) Insertions. (D) Deletions.
Fig 2.
Error rates of variant-calling pipelines.
The fraction of (A) false-positive (FP) and (B) mismatch (MM) mutation calls as a percentage of the total number of variants called by each pipeline. Variant callers are indicated as in Fig 1. Color codes for different categories of variants are indicated by the key (inset). Abbreviations: struct, structural variant; hom, homozygous; het, heterozygous; del, deletion; ins, insertion; SNP, single-nucleotide polymorphism.
Fig 3.
Sensitivity of variant-calling pipelines for Hawaiian SNPs.
(A) Plot of Hawaiian (Haw) SNP fraction vs. physical map position using the default threshold for variant calling. Shown is a representative example used to map lin-9(n112), located on chromosome III at position 8.9 Mb (red arrow), with BBMap+FreeBayes for variant calling. Green line, LOESS regression of the SNP fraction. (B) The same data as A with a minimum threshold of 1% variant call and one supporting read for FreeBayes. Mapping data from [26]. (C) Sensitivity for 50% (blue) and 5% (red) Hawaiian SNPs. The percentage of true-positive (TP) Hawaiian SNP calls are indicated for each pipeline. Variant callers are indicated as in Fig 1.