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 66 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 1,635,488 | 1 | . | C | 60.6% | 358.1 / 285.6 | 183 | intergenic (‑255/+174) | PA14_RS07605/pldA | T6SS immunity protein Tli4 family protein/phospholipase D |
| * | NC_008463 | 603,087 | 1 | . | G | 52.2% | inf / inf | 538 | intergenic (+179/‑160) | PA14_RS02785/PA14_RS02790 | helix‑turn‑helix transcriptional regulator/FAD‑binding oxidoreductase |
| * | NC_008463 | 5,536,163 | 0 | G | A | 47.6% | 369.6 / inf | 427 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 44.2% | 865.1 / inf | 745 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 5,398,025 | 0 | T | C | 44.0% | 382.3 / inf | 494 | intergenic (‑52/+47) | PA14_RS24735/PA14_RS24740 | ATP‑binding protein/TraR/DksA family transcriptional regulator |
| * | NC_008463 | 1,710,769 | 1 | . | C | 43.9% | 22.9 / inf | 550 | coding (818/2484 nt) | PA14_RS07945 | LuxR C‑terminal‑related transcriptional regulator |
| * | NC_008463 | 203,878 | 0 | A | G | 43.5% | 468.9 / inf | 552 | M271T (ATG→ACG) | cttP | trichloroethylene chemotactic transducer CttP |
| * | NC_008463 | 5,094,701 | 0 | C | T | 43.2% | 154.5 / inf | 620 | G184S (GGC→AGC) | PA14_RS23315 | Nudix family hydrolase |
| * | NC_008463 | 1,660,913 | 0 | G | . | 42.1% | inf / inf | 465 | coding (1169/1368 nt) | PA14_RS07710 | MFS transporter |
| * | NC_008463 | 892,764 | 0 | G | A | 42.1% | 202.8 / inf | 582 | S318S (AGC→AGT) | PA14_RS04185 | peptidase domain‑containing ABC transporter |
| * | NC_008463 | 4,458,790 | 0 | G | A | 42.1% | 216.1 / inf | 615 | R253W (CGG→TGG) | fleR | sigma‑54‑dependent response regulator transcription factor FleR |
| * | NC_008463 | 1,660,914 | 0 | C | . | 41.9% | inf / inf | 466 | coding (1168/1368 nt) | PA14_RS07710 | MFS transporter |
| * | NC_008463 | 934,247 | 0 | A | G | 40.6% | 518.5 / inf | 475 | Y92C (TAC→TGC) | ampR | LysR family transcriptional regulator AmpR |
| * | NC_008463 | 114,794 | 0 | A | G | 40.3% | 943.8 / inf | 806 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,636,538 | 1 | . | G | 40.1% | 148.6 / inf | 338 | coding (110/606 nt) | PA14_RS12415 | 3‑mercaptopropionate dioxygenase |
| * | NC_008463 | 1,861,283 | 0 | C | T | 39.6% | 314.6 / inf | 533 | L212L (CTG→TTG) | PA14_RS08630 | DUF4123 domain‑containing protein |
| * | NC_008463 | 5,220,067 | 1 | . | G | 37.8% | 322.3 / inf | 434 | coding (267/681 nt) | PA14_RS23890 | Fe2+‑dependent dioxygenase |
| * | NC_008463 | 4,616,454 | 0 | T | G | 33.6% | 272.1 / 24.7 | 158 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 33.1% | 880.7 / inf | 545 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 31.4% | 693.6 / inf | 548 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 400 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 530 (1.050) | 25 (0.060) | 24/256 | 26.4 | 5.1% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 472 (1.090) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473590 | 624 (1.240) | 19 (0.040) | 16/258 | 30.5 | 3.4% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 537 (1.230) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 3304506 | 427 (0.850) | 14 (0.030) | 13/266 | 32.7 | 3.5% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 400 (0.890) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 419388 | 522 (1.040) | 14 (0.030) | 14/276 | 32.8 | 2.8% | coding (1484/1734 nt) | ggt | gamma‑glutamyltransferase |
| ? | NC_008463 | 419804 = | 488 (1.050) | coding (1068/1734 nt) | ggt | gamma‑glutamyltransferase | |||||
| * | ? | NC_008463 | = 1707447 | 523 (1.040) | 14 (0.030) | 13/270 | 33.0 | 2.9% | coding (830/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein |
| ? | NC_008463 | 1707841 = | 475 (1.040) | coding (1224/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein | |||||
| * | ? | NC_008463 | = 5884344 | 539 (1.070) | 12 (0.030) | 12/272 | 33.7 | 2.1% | coding (746/1425 nt) | hldE | bifunctional D‑glycero‑beta‑D‑manno‑heptose‑7‑phosphate kinase/D‑glycero‑beta‑D‑manno‑heptose 1‑phosphate adenylyltransferase HldE |
| ? | NC_008463 | 5884597 = | 607 (1.320) | coding (493/1425 nt) | hldE | bifunctional D‑glycero‑beta‑D‑manno‑heptose‑7‑phosphate kinase/D‑glycero‑beta‑D‑manno‑heptose 1‑phosphate adenylyltransferase HldE | |||||
| * | ? | NC_008463 | = 44749 | 623 (1.240) | 12 (0.030) | 11/266 | 34.0 | 2.5% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 387 (0.860) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||
| * | ? | NC_008463 | = 44749 | 623 (1.240) | 12 (0.030) | 11/266 | 34.0 | 2.5% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 45182 = | 396 (0.880) | coding (2249/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 804437 | 450 (0.890) | 11 (0.020) | 11/272 | 34.4 | 2.4% | coding (477/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter |
| ? | NC_008463 | 804780 = | 503 (1.090) | coding (820/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter | |||||
| * | ? | NC_008463 | = 33046 | 533 (1.060) | 11 (0.020) | 11/278 | 34.7 | 2.1% | coding (1487/1512 nt) | betC | choline‑sulfatase |
| ? | NC_008463 | 33603 = | 550 (1.170) | coding (930/1512 nt) | betC | choline‑sulfatase | |||||