Fig. 3: F1 accuracy by tuning different evaluation parameters and distribution of breakpoint shift and alternate allele sequence similarity for SVs on Hifi_L1. | Nature Communications

Fig. 3: F1 accuracy by tuning different evaluation parameters and distribution of breakpoint shift and alternate allele sequence similarity for SVs on Hifi_L1.

From: Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data

Fig. 3

a Grid search heatmap of F1 values for deletion SVs by different read alignment-based tools. O is the minimum reciprocal overlap between SV call and gold standard SV. p is the minimum percentage of allele sequence similarity between SV call and gold standard SV. O and p vary from 0–1 with a 0.1 interval. b Grid search F1 heatmap for deletion SVs by different assembly-based tools. c Distribution of breakpoint shift for deletion SVs. d Distribution of alternate sequence similarity for deletion SVs. e Grid search F1 heatmap for insertion SVs by different read alignment-based tools. r is the maximum reference ___location distance between SV call and gold standard SV. p is the minimum percentage of allele sequence similarity between SV call and gold standard SV. p vary from 0–1 with a 0.1 interval. r varies from 0–1000 bp with a 100 bp interval. f Grid search F1 heatmap for insertion SVs by different assembly-based tools. g Distribution of breakpoint shift for insertion SVs. h Distribution of alternate sequence similarity for insertion SVs. Source data are provided as a Source Data file.

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