| Size of sequenced reference genome (bp) |
39,686,251 |
31,546,591 |
| Number of exonic sites in reference genome (bp) |
17,296,247 (43.6%) |
15,570,421 (49.4%) |
| Number of haplotypes |
13 |
17 |
| Summary genome alignment |
Total alignment length (Mb) |
Number of alignment blocks |
Total alignment length (Mb) |
Number of alignment blocks |
| MultiZ alignment |
40.8 |
21,500 |
32.4 |
22,296 |
| Splitting in maximum 10 kb |
40.8 |
21,904 |
32.4 |
23,001 |
| MAFFT realignment |
40.5 |
21,904 |
32.2 |
23,001 |
| Keep blocks with all strains |
27.7 |
6,445 |
28.2 |
7,117 |
| Filter 1 |
27.5 |
15,703 |
28.0 |
18,402 |
| Filter 2 |
27.3 |
18,785 |
27.7 |
26,074 |
| Percentage of repeated sequences in initial alignment (%) |
19.74 |
3.36 |
| Percentage of repeated sequences in final alignment (%) |
0.93 |
1.38 |
| Total number of SNPs |
1,483,950 |
1,069,014 |
| Total number of analyzed SNPs (biallelic, no unresolved state) and percent of total SNPs |
1,438,385 (96.9%) |
1,035,158 (96.8%) |
| Total number of SNPs in exons and percent of total SNPs |
713,733 (48.1%) |
403,895 (37.8%) |
| Total number of analyzed SNPs in exons (biallelic, no unresolved state), and percent of total analyzed SNPs in exons |
690,096 (96.7%) |
396,247 (98.1%) |
| Summary SNP analyses |
1-Mb windows |
100-kb windows |
1-Mb windows |
100-kb windows |
| Minimum number of SNPs |
143 |
0 |
0 |
0 |
| Median number of SNPs |
43,680 |
3,556 |
1,598 |
634 |
| Maximum number of SNPs |
1,02,400 |
15,170 |
33,680 |
20,110 |
| Diversity (median of Watterson’s θ in windows of 10 kb) |
0.0139 |
0.008663 |
