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 72 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 933,109 | 0 | A | G | 71.9% | 820.3 / inf | 528 | V239A (GTC→GCC) | PA14_RS04350 | class C beta‑lactamase PDC‑34 |
| * | NC_008463 | 1,635,488 | 1 | . | C | 71.6% | 452.0 / 220.1 | 205 | intergenic (‑255/+174) | PA14_RS07605/pldA | T6SS immunity protein Tli4 family protein/phospholipase D |
| * | NC_008463 | 6,206,069 | 0 | T | G | 48.7% | 618.0 / inf | 692 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 5,536,163 | 0 | G | A | 48.5% | 344.9 / inf | 436 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 43.2% | 898.7 / inf | 755 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.7% | 533.6 / inf | 521 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 6,028,958 | 0 | T | C | 31.9% | 1090.1 / inf | 576 | D346G (GAC→GGC) | PA14_RS27545 | DUF3999 domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 31.9% | 237.5 / 29.6 | 123 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 2,855,256 | 0 | A | G | 31.7% | 610.1 / inf | 364 | N2230S (AAC→AGC) | PA14_RS13370 | hemagglutinin repeat‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 31.6% | 1576.6 / inf | 735 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 1,538,683 | 0 | A | G | 31.4% | 974.0 / inf | 515 | Y40C (TAC→TGC) | PA14_RS07195 | alpha/beta hydrolase |
| * | NC_008463 | 3,994,253 | 0 | C | . | 31.3% | 1286.4 / inf | 469 | intergenic (+121/+121) | PA14_RS18210/uraH | solute carrier family 23 protein/hydroxyisourate hydrolase |
| * | NC_008463 | 4,437,014 | 0 | A | G | 31.0% | 1039.3 / inf | 540 | D102G (GAC→GGC) | PA14_RS20265 | OmpA family protein |
| * | NC_008463 | 3,878,203 | 0 | A | G | 30.4% | 961.9 / inf | 479 | L254P (CTG→CCG) | PA14_RS17690 | alpha/beta hydrolase |
| * | NC_008463 | 5,114,133 | 0 | T | C | 30.2% | 1217.2 / inf | 605 | T192A (ACC→GCC) | PA14_RS23395 | UDP‑N‑acetylmuramoyl‑tripeptide‑‑D‑alanyl‑D‑ alanine ligase |
| * | NC_008463 | 6,229,975 | 0 | C | T | 30.1% | 749.5 / inf | 553 | R528C (CGC→TGC) | betT | choline BCCT transporter BetT |
| * | NC_008463 | 5,224,866 | 0 | T | C | 29.8% | 819.4 / inf | 406 | Y40C (TAC→TGC) | PA14_RS23910 | type III PLP‑dependent enzyme |
| * | NC_008463 | 1,046,795 | 0 | A | G | 29.8% | 991.5 / inf | 488 | T230A (ACC→GCC) | PA14_RS04895 | D‑alanyl‑D‑alanine carboxypeptidase family protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 29.7% | 659.7 / 46.9 | 315 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,143,572 | 0 | T | C | 29.1% | 702.8 / 294.0 | 335 | I391T (ATC→ACC) | PA14_RS18895 | phospholipase D‑like domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 365 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 473590 | 616 (1.250) | 30 (0.070) | 25/260 | 25.1 | 5.5% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 501 (1.170) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5935541 | 527 (1.070) | 22 (0.050) | 22/258 | 26.3 | 4.5% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 475 (1.120) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 704259 | 513 (1.040) | 17 (0.040) | 16/264 | 29.7 | 3.3% | coding (849/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein |
| ? | NC_008463 | 704746 = | 532 (1.230) | coding (1336/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein | |||||
| * | ? | NC_008463 | = 229722 | 525 (1.060) | 14 (0.030) | 14/270 | 31.2 | 2.7% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 530 (1.190) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 581520 | 529 (1.070) | 12 (0.030) | 12/270 | 32.4 | 2.6% | coding (1050/1482 nt) | nirN | dihydro‑heme d1 dehydrogenase |
| ? | NC_008463 | 581932 = | 430 (0.970) | coding (638/1482 nt) | nirN | dihydro‑heme d1 dehydrogenase | |||||
| * | ? | NC_008463 | = 3143295 | 448 (0.910) | 12 (0.030) | 11/268 | 32.9 | 2.8% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 421 (0.960) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||
| * | ? | NC_008463 | = 3441406 | 400 (0.810) | 12 (0.030) | 11/270 | 33.0 | 3.0% | coding (1196/1431 nt) | hbcR | sigma‑54‑dependent transcriptional regulator HbcR |
| ? | NC_008463 | 3442019 = | 413 (0.930) | coding (102/1392 nt) | PA14_RS15680 | GntP family permease | |||||
| * | ? | NC_008463 | = 100189 | 562 (1.140) | 10 (0.020) | 10/268 | 33.5 | 2.0% | coding (759/1497 nt) | tssC | type VI secretion system contractile sheath large subunit |
| ? | NC_008463 | 100610 = | 485 (1.100) | coding (1180/1497 nt) | tssC | type VI secretion system contractile sheath large subunit | |||||
| * | ? | NC_008463 | = 2085818 | 495 (1.000) | 12 (0.030) | 11/280 | 33.6 | 2.7% | coding (951/1509 nt) | xcpR | GspE family T2SS ATPase variant XcpR |
| ? | NC_008463 | 2086152 = | 396 (0.860) | coding (1285/1509 nt) | xcpR | GspE family T2SS ATPase variant XcpR | |||||
| * | ? | NC_008463 | 5127042 = | 394 (0.800) | 12 (0.030) | 11/284 | 33.8 | 3.1% | coding (783/1212 nt) | PA14_RS23465 | cytochrome bc complex cytochrome b subunit |
| ? | NC_008463 | = 5127038 | 373 (0.800) | coding (787/1212 nt) | PA14_RS23465 | cytochrome bc complex cytochrome b subunit | |||||