Fig. 2
From: Evaluation of variant calling tools for large plant genome re-sequencing
Comparison of mapping tools. The raw sequence read fastq file (raw) and the preprocessed trimmed (trim), or duplicate removal (rep1) fastq files were mapped onto wheat reference genome v1.0 by Bowtie2 or BWA-mem. The mapping statistics were calculated by Samtools using different flags. The Y-axis represents the percentage of read counts among total raw reads. a. The percentage of total mapped reads in six different experiments (two mapping tools and three data preprocesses) among total raw read number. b. The percentage of unmapped read number. c. The percentage of properly paired mapped reads whose reads R1 and R2 from the same segment are mapped on the same chromosome at a good expected distance with the correct directions. d. The percentage of read number greater than mapping quality (MQ) of 10. e. The percentage of mapped read numbers that had MQ greater than 10 and mismatched bases less than 10 per read