mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 42 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 1,026,510 | 0 | C | . | 57.6% | ‑2.0 / inf | 485 | coding (105/1356 nt) | mpl | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase |
| * | NC_008463 | 5,536,163 | 0 | G | A | 54.9% | 203.6 / inf | 416 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 45.8% | 906.3 / inf | 884 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 6,206,069 | 0 | T | G | 44.5% | 913.1 / inf | 822 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 5,461,009 | 0 | A | G | 40.7% | 609.6 / inf | 491 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 40.0% | 684.9 / inf | 524 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 36.3% | 1439.3 / inf | 788 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 31.5% | 596.1 / inf | 508 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 30.7% | 346.6 / 18.4 | 167 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 29.5% | 248.6 / 58.7 | 156 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 1,026,509 | 0 | A | C | 27.9% | 1139.0 / inf | 516 | Y35S (TAC→TCC) | mpl | UDP‑N‑acetylmuramate:L‑alanyl‑gamma‑D‑glutamyl‑ meso‑diaminopimelate ligase |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.2% | 458.9 / 21.5 | 297 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 26.1% | 783.7 / 38.7 | 338 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 5,460,283 | 0 | A | G | 25.5% | 1075.6 / inf | 492 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 3,630,825 | 0 | G | T | 24.3% | 346.0 / 31.5 | 206 | intergenic (+16/‑259) | tse1/metH | type VI secretion system effector peptidoglycanhydrolase Tse1/methionine synthase |
| * | NC_008463 | 2,621,464 | 0 | A | T | 23.9% | 836.3 / 55.2 | 395 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 2,954,003 | 0 | T | G | 23.8% | 1073.9 / 40.8 | 447 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 1,763,606 | 0 | T | A | 23.7% | 143.3 / 11.7 | 118 | L37H (CTC→CAC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 23.4% | 1260.3 / 75.7 | 441 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 5,386,384 | 0 | A | C | 23.3% | 1271.9 / 29.2 | 430 | L227R (CTG→CGG) | proB | glutamate 5‑kinase |
| Marginal new junction evidence (lowest skew 10 of 459 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5978234 | 396 (0.750) | 122 (0.240) | 89/284 | 11.5 | 24.6% | coding (37/426 nt) | tatB | Sec‑independent protein translocase protein TatB |
| ? | NC_008463 | 5978244 = | 373 (0.740) | coding (47/426 nt) | tatB | Sec‑independent protein translocase protein TatB | |||||
| * | ? | NC_008463 | = 704259 | 570 (1.080) | 17 (0.040) | 16/264 | 32.1 | 3.2% | coding (849/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein |
| ? | NC_008463 | 704746 = | 536 (1.150) | coding (1336/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein | |||||
| * | ? | NC_008463 | = 473590 | 604 (1.140) | 19 (0.040) | 15/260 | 32.4 | 3.5% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 518 (1.130) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 6439354 | 595 (1.120) | 13 (0.030) | 13/260 | 33.6 | 2.6% | coding (973/1290 nt) | PA14_RS29425 | MFS transporter |
| ? | NC_008463 | 6439844 = | 462 (1.010) | coding (483/1290 nt) | PA14_RS29425 | MFS transporter | |||||
| * | ? | NC_008463 | = 4056257 | 456 (0.860) | 13 (0.030) | 13/260 | 33.6 | 3.1% | coding (935/2262 nt) | PA14_RS18515 | chemotaxis protein CheA |
| ? | NC_008463 | 4056561 = | 406 (0.880) | coding (631/2262 nt) | PA14_RS18515 | chemotaxis protein CheA | |||||
| * | ? | NC_008463 | = 5935541 | 542 (1.020) | 14 (0.030) | 12/258 | 34.1 | 3.0% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 443 (0.970) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 229722 | 540 (1.020) | 14 (0.030) | 13/270 | 34.3 | 2.9% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 438 (0.920) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 5813856 | 542 (1.020) | 16 (0.030) | 13/272 | 34.4 | 3.1% | coding (900/1293 nt) | PA14_RS26670 | adenylosuccinate synthase |
| ? | NC_008463 | 5814373 = | 522 (1.090) | coding (383/1293 nt) | PA14_RS26670 | adenylosuccinate synthase | |||||
| * | ? | NC_008463 | = 1030391 | 682 (1.290) | 12 (0.030) | 12/262 | 34.4 | 2.0% | coding (733/1740 nt) | PA14_RS04810 | C13 family peptidase |
| ? | NC_008463 | 1030737 = | 585 (1.260) | coding (387/1740 nt) | PA14_RS04810 | C13 family peptidase | |||||
| * | ? | NC_008463 | = 6418952 | 495 (0.930) | 12 (0.030) | 12/264 | 34.5 | 2.8% | coding (634/1629 nt) | PA14_RS29320 | glycosyltransferase |
| ? | NC_008463 | 6419205 = | 403 (0.860) | coding (887/1629 nt) | PA14_RS29320 | glycosyltransferase | |||||