Define regions of difference (RDs or SNPs) by comparing genomes of six isolates to a published F. tularensis Schu S4 genomic sequence.
Francisella tularensis Schu S4: GenBank AJ749949.2
- Francisella tularensis Schu S4 FSC043
- Francisella tularensis Schu S4 FTS-634/635
- Francisella tularensis Schu S4 NR-10492
- Francisella tularensis Schu S4 NR-28534
- Francisella tularensis Schu S4 NR-643
- Francisella tularensis Schu S4 SL
You can find the table of regions of difference in RD.html
You can see the complete list of 17 SNPs and 4498 INDELs RD_full.html
You can find a detailed report in report.md.
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NJ tree based on GSNP counts (SNPs that have 20 identical base pairs that flank them)
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NJ tree based on aligned 4515 variant bases
| Isolate_name | SNPs (NCBI assembly) | SNPs (reads: Pond lib) | SNPs (reads: Solexa lib) | Ref bases with no read coverage |
|---|---|---|---|---|
| FSC043 | 1 | 0/0 | 0/0 | 0 |
| FTS-634 | 8 | 6/6 | 6/6 | 0 |
| NR-10492 | 1 | 0/0 | 0/1 | 0 |
| NR-28534 | 2 | 0/0 | 0/2 | 0 |
| NR-643 | 8 | 7/7 | 10/11 | 0 |
| SL | 10 | 0/0 | 0/1 | 298 (0.016%) |
Each isolate is associated with two paired-end libraries. The number
of SNPs estimated through read mapping is shown in the format of # filterd SNPs / # raw SNPs. The minimum variant fraction for filtered
SNPs is 0.3.
- vcf/: Raw SNPs estimated by read mapping (BWA-mem v0.7.7, Samtools v0.1.19)
- snps/: Annotated filtered SNPs
- bbhs/: Protein-protein bidiretional best hits and unique proteins (reference vs de novo assemblies, both annotated using RAST)
- mummer/: DNA-level difference computed using Mummer (reference vs de novo assemblies)
- uncov/: Base positions in the reference contigs with no read coverage (empty if none)
- assembly/: De novo assemblies computed using Assembly-RAST (with --recipe "rast")
- rast2/: RAST2 annotations of de novo assembled contigs
- olive-mummer/: SNPs estimated by comparing reference and NCBI scaffolds downloaded from the Olive data portal of Broad Institute.
- mugsy/: Whole-genome DNA alignment of all NCBI scaffolds and reference using Mugsy
- trees/: Phylogenetic trees of the seven isolates