Skip to main content

Table 1 Variant calling statistics, considering strain-specific reads and considering total reads produced

From: Landscape of genomic diversity and host adaptation in Fusarium graminearum

Isolate INRA-156 INRA-159 INRA-164 INRA-171 INRA-181 INRA-195 Totala
% of reference genome callableb 97.7% 97.7% 97.6% 97.6% 97.5% 97.7% 98.3%
Number of SNPs 144,679 146,849 144,802 143,283 145,071 145,840 234,151
Number of InDels 4,929 5,073 4,953 4,844 4,938 4,970 8,605
Total number of variants 149,608 151,922 149,755 148,127 150,009 150,810 242,756
Mean depth of sequencing at variant position (X) 72.3 83.5 78.0 79.5 79.6 80.3 78.9
Mean variant density (variants per kb) 3.9 4.0 3.9 3.9 3.9 4.0 6.4
Number of exonic variants 70,850 71,488 70,259 69,130 70,659 71,676 111,975
Number of intronic variants 10,779 10,821 10,509 10,320 10,682 10,786 17,095
Number of non-genic variants 67,979 69,613 68,987 68,677 68,668 68,348 113,686
Number of variants with French genomes 66,726 69,040 66,873 65,245 67,127 67,928 159,874
  1. a: considering all reads produced by whole genome sequencing of the six isolates
  2. b: exluding the end of the chromosome IV from 7,953,943 bp onwards, corresponding to repeated RNA encoding sequence (see Methods)