Reads | Assembler | Contig | Scaffold | Transf | Untransf | Shared | Masked |
|---|
Sim | allp | 57 | 7 | 21 | 1 | 18 | 12 |
Sim | sga_m75 | 504 | 463 | NA | NA | NA | NA |
Sim | sga_m77 | 513 | 479 | NA | NA | NA | NA |
Sim | soap_K69 | 1481 | 698 | 255 | 451 | 137 | 44 |
Sim | soap_K71 | 1469 | 769 | NA | NA | NA | NA |
Bs-1 | allp | 66 | 9 | 35 | 0 | 23 | 15 |
Bs-1 | sga_m75 | 899 | 711 | NA | NA | NA | NA |
Bs-1 | sga_m77 | 871 | 687 | NA | NA | NA | NA |
Bs-1 | soap_K69 | 1916 | 670 | 365 | 429 | 210 | 95 |
Bs-1 | soap_K71 | 1909 | 692 | NA | NA | NA | NA |
- Reads column indicates the origin of aligned reads: ‘Sim’ refers to the simulated paired-end reads while ‘Bs-1’ denotes the actual A. thaliana Bs-1 short-insert library [21]. Contig and Scaffold columns show the number of SNPs at position k in the respective contig and scaffold assemblies. ‘Transf’ column shows the number of SNPs at position k called against scaffolds after the scaffold coordinates were transformed to contig coordinates. Only Sim_allp and Sim_soap_K69 scaffold coordinates were transformed. ‘Untransf’ column indicates the number of SNPs that failed to transform because of contig length threshold (Sim_soap_K69) or scaffold being extended beyond the length specified in the assembler’s scaffold map (Sim_allp). ‘Shared’ column reports the number of SNPs present in both Contig and Tranformed sets. ‘Masked’ column shows the SNPs that appear in Contig and Transformed but not in Scaffold because of the change in their relative positions. All counts except ‘Untransf’ are for SNPs in position k
