PRJNA275974
Report summary ▲
| Isolates | Author | Date | Host | Folder |
|---|---|---|---|---|
| 6 | tseemann | Sun May 29 19:10:30 2016 | 526080-s598784 | /home/tseemann/git/nullarbor/demo/nullarbor |
Sequence data ▲
| Isolate | Reads | Yield | GeeCee | MinLen | AvgLen | MaxLen | ModeLen | Phred | AvgQual | Depth | Quality |
|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR1922797 | 1656408 | 388360973 | 48.7 | 30 | 234 | 250 | 250 | 33 | 33.8 | 81x | ✔ |
| SRR1922795 | 2454352 | 581858593 | 48.7 | 31 | 237 | 250 | 250 | 33 | 35.1 | 122x | ✔ |
| SRR1922793 | 2506916 | 578000020 | 48.8 | 31 | 230 | 250 | 250 | 33 | 33.7 | 121x | ✔ |
| SRR1922796 | 2570150 | 605635335 | 48.7 | 30 | 235 | 250 | 250 | 33 | 34.8 | 127x | ✔ |
| SRR1922792 | 2070010 | 481023858 | 48.9 | 33 | 232 | 250 | 250 | 33 | 34.3 | 100x | ✔ |
| SRR1922794 | 2391206 | 559626424 | 48.7 | 31 | 234 | 250 | 250 | 33 | 34.8 | 117x | ✔ |
Species identification ▲
| Isolate | #1 Match | % | #2 Match | % | #3 Match | % | #4 Match | % | Quality |
|---|---|---|---|---|---|---|---|---|---|
| SRR1922797 | Yersinia pseudotuberculosis | 42.04 | unclassified | 7.33 | Yersinia pestis | 1.19 | Yersinia enterocolitica | 0.29 | ✘ |
| SRR1922795 | Yersinia pseudotuberculosis | 48.03 | unclassified | 0.90 | Yersinia pestis | 0.06 | Yersinia enterocolitica | 0.02 | ✘ |
| SRR1922793 | Yersinia pseudotuberculosis | 40.50 | unclassified | 6.91 | Yersinia pestis | 1.13 | Serratia plymuthica | 0.23 | ✘ |
| SRR1922796 | Yersinia pseudotuberculosis | 44.44 | unclassified | 3.06 | Yersinia pestis | 1.21 | Yersinia enterocolitica | 0.20 | ✘ |
| SRR1922792 | Yersinia pseudotuberculosis | 41.64 | unclassified | 6.17 | Yersinia pestis | 1.34 | Serratia plymuthica | 0.23 | ✘ |
| SRR1922794 | Yersinia pseudotuberculosis | 43.99 | unclassified | 3.03 | Yersinia pestis | 1.15 | Yersinia enterocolitica | 0.18 | ✘ |
MLST ▲
| Isolate | Scheme | Sequence Type | Allele | Allele | Allele | Allele | Allele | Allele | Allele | Quality |
|---|---|---|---|---|---|---|---|---|---|---|
| SRR1922792 | ypseudotuberculosis | 166 | adk(33) | argA(2) | aroA(1) | glnA(2) | thrA(5) | tmk(6) | trpE(1) | ✔ |
| SRR1922793 | ypseudotuberculosis | 166 | adk(33) | argA(2) | aroA(1) | glnA(2) | thrA(5) | tmk(6) | trpE(1) | ✔ |
| SRR1922794 | ypseudotuberculosis | 14 | adk(1) | argA(2) | aroA(1) | glnA(2) | thrA(5) | tmk(6) | trpE(1) | ✔ |
| SRR1922795 | ypseudotuberculosis | 42 | adk(1) | argA(2) | aroA(1) | glnA(2) | thrA(8) | tmk(2) | trpE(1) | ✔ |
| SRR1922796 | ypseudotuberculosis | 14 | adk(1) | argA(2) | aroA(1) | glnA(2) | thrA(5) | tmk(6) | trpE(1) | ✔ |
| SRR1922797 | ypseudotuberculosis | 14 | adk(1) | argA(2) | aroA(1) | glnA(2) | thrA(5) | tmk(6) | trpE(1) | ✔ |
Resistome ▲
| Isolate | Found |
|---|---|
| SRR1922797 | 0 |
| SRR1922795 | 0 |
| SRR1922793 | 0 |
| SRR1922796 | 0 |
| SRR1922792 | 0 |
| SRR1922794 | 0 |
Assembly and annotation ▲
| Isolate | Contigs | bp | ok | Ns | gaps | min | avg | max | N50 | Insert size (25,50,75)% | CDS | rRNA | tRNA | tmRNA | Quality |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR1922792 | 481 | 4940320 | 4940320 | 0 | 0 | 502 | 10270 | 118654 | 26590 | (273, 424, 576) | 4310 | 2 | 70 | 1 | ✔ |
| SRR1922793 | 483 | 4912604 | 4912604 | 0 | 0 | 500 | 10171 | 146641 | 26143 | (258, 395, 532) | 4268 | 2 | 67 | 1 | ✔ |
| SRR1922794 | 456 | 4721086 | 4721086 | 0 | 0 | 501 | 10353 | 105997 | 24809 | (282, 416, 550) | 4075 | 2 | 68 | 1 | ✔ |
| SRR1922795 | 420 | 4568376 | 4568376 | 0 | 0 | 501 | 10877 | 119302 | 23279 | (314, 436, 556) | 3916 | 1 | 68 | 1 | ✔ |
| SRR1922796 | 486 | 4740719 | 4740719 | 0 | 0 | 501 | 9754 | 132743 | 22249 | (299, 429, 558) | 4090 | 68 | 1 | ✔ | |
| SRR1922797 | 458 | 5147646 | 5147646 | 0 | 0 | 501 | 11239 | 130717 | 33195 | (280, 424, 574) | 4569 | 3 | 69 | 1 | ✔ |
Reference genome ▲
| Sequence | Length | Description |
|---|---|---|
| NC_010465 | 4689441 | Yersinia pseudotuberculosis YPIII chromosome, complete genome. |
| TOTAL | 4689441 | Total reference size in bp |
Core genome ▲
| Isolate | Aligned Bases | Reference bases | % Aligned Bases | Quality |
|---|---|---|---|---|
| SRR1922792 | 4333977 | 4689441 | 92.42 | ✔ |
| SRR1922793 | 4359399 | 4689441 | 92.96 | ✔ |
| SRR1922794 | 4348834 | 4689441 | 92.74 | ✔ |
| SRR1922795 | 4293587 | 4689441 | 91.56 | ✔ |
| SRR1922796 | 4352849 | 4689441 | 92.82 | ✔ |
| SRR1922797 | 4387422 | 4689441 | 93.56 | ✔ |
| AVERAGE | 4346011 | 4689441 | 92.68 | ✔ |
Pairwise core SNP distances ▲
| ID | Reference
| SRR1922792
| SRR1922793
| SRR1922794
| SRR1922795
| SRR1922796
| SRR1922797
|
|---|---|---|---|---|---|---|---|
| Reference | 0 | 6420 | 6409 | 6037 | 14394 | 6027 | 6079 |
| SRR1922792 | 6420 | 0 | 67 | 1923 | 16260 | 1921 | 3601 |
| SRR1922793 | 6409 | 67 | 0 | 1938 | 16253 | 1938 | 3626 |
| SRR1922794 | 6037 | 1923 | 1938 | 0 | 15977 | 28 | 3404 |
| SRR1922795 | 14394 | 16260 | 16253 | 15977 | 0 | 15985 | 16079 |
| SRR1922796 | 6027 | 1921 | 1938 | 28 | 15985 | 0 | 3402 |
| SRR1922797 | 6079 | 3601 | 3626 | 3404 | 16079 | 3402 | 0 |
Pan genome ▲
| Ortholog class | Definition | Count |
|---|---|---|
| Core genes | (99% <= strains <= 100%) | 3438 |
| Soft core genes | (95% <= strains < 99%) | 0 |
| Shell genes | (15% <= strains < 95%) | 2068 |
| Cloud genes | (0% <= strains < 15%) | 0 |
| Total genes | (0% <= strains <= 100%) | 5506 |
Software versions ▲
| Tool | Version |
|---|---|
| Abricate | 0.3 |
| BWA MEM | 0.7.13-r1126 |
| FastTree | 2.1.8 Double precision (No SSE3), OpenMP (8 threads): |
| FreeBayes | 1.0.2-dirty |
| Kraken | 0.10.5-beta |
| MLST | 2.6 |
| MegaHit | 1.0.3 |
| Newick-Utils | (unable to determine version) |
| Nullarbor | 1.20 |
| Prokka | 1.12-beta |
| Roary | 6.2 |
| SAMtools | 1.3 |
| SPAdes | 3.7.1 |
| Snippy | 3.0 |
| Trimmomatic | (unable to determine version) |
About ▲
- This primary author of Nullarbor is Torsten Seemann.
- You can download the software from Github.
- Please report bugs at the Nullarbor Issue Tracker.
- If you use Nullarbor please use the latest citation.