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 41 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 6,206,069 | 0 | T | G | 55.6% | 306.5 / inf | 717 | 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 | 45.9% | 376.4 / inf | 396 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 43.3% | 805.1 / inf | 875 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 34.0% | 568.5 / inf | 496 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 32.9% | 1368.5 / inf | 758 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.9% | 845.1 / inf | 477 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 30.7% | 305.5 / 20.1 | 170 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 30.4% | 811.5 / inf | 434 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 6,206,227 | 0 | G | A | 29.3% | 139.6 / 81.6 | 82 | H128H (CAC→CAT) | PA14_RS28350 | Hcp family type VI secretion system effector |
| * | NC_008463 | 5,910,256 | 0 | A | C | 28.7% | 647.9 / 42.3 | 291 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,347,580 | 0 | T | G | 28.3% | 762.8 / 21.7 | 376 | intergenic (‑79/+150) | PA14_RS19855/PA14_RS19860 | hypothetical protein/zonular occludens toxin family protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 27.7% | 317.4 / 18.6 | 162 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 26.8% | 665.5 / 59.8 | 317 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 25.5% | 1031.2 / 92.0 | 392 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 2,954,003 | 0 | T | G | 25.0% | 933.2 / 44.7 | 409 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 5,109,194 | 0 | T | G | 24.6% | 1088.2 / 59.4 | 404 | D169A (GAC→GCC) | murG | undecaprenyldiphospho‑muramoylpentapeptide beta‑N‑acetylglucosaminyltransferase |
| * | NC_008463 | 5,125,799 | 0 | T | G | 24.4% | 311.4 / 31.8 | 229 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 5,248,950 | 0 | T | G | 23.9% | 921.9 / 13.5 | 375 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 2,621,464 | 0 | A | T | 23.9% | 934.5 / 60.5 | 420 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 1,763,534 | 0 | T | G | 23.8% | 495.2 / 21.5 | 308 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| Marginal new junction evidence (lowest skew 10 of 495 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 517 (1.030) | 26 (0.060) | 24/256 | 29.4 | 5.5% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 450 (1.040) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473590 | 623 (1.240) | 26 (0.060) | 24/258 | 29.6 | 4.8% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 492 (1.130) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 229722 | 466 (0.930) | 19 (0.040) | 19/268 | 32.8 | 4.2% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 452 (1.000) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 44749 | 544 (1.080) | 17 (0.040) | 16/266 | 34.4 | 3.8% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 379 (0.850) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||
| * | ? | NC_008463 | = 44749 | 544 (1.080) | 17 (0.040) | 16/266 | 34.4 | 3.7% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 45182 = | 399 (0.890) | coding (2249/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 1707447 | 547 (1.090) | 16 (0.040) | 15/270 | 35.3 | 3.1% | coding (830/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein |
| ? | NC_008463 | 1707841 = | 490 (1.080) | coding (1224/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein | |||||
| * | ? | NC_008463 | = 2053197 | 275 (0.550) | 16 (0.030) | 14/278 | 36.5 | 5.7% | intergenic (+48/‑1) | PA14_RS09545/PA14_RS09550 | tRNA‑Ala/tRNA‑Glu |
| ? | NC_008463 | 2053486 = | 276 (0.590) | intergenic (+44/‑3) | PA14_RS09555/PA14_RS09560 | tRNA‑Ala/tRNA‑Glu | |||||
| * | ? | NC_008463 | = 804437 | 528 (1.050) | 13 (0.030) | 13/272 | 36.7 | 2.7% | coding (477/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter |
| ? | NC_008463 | 804780 = | 446 (0.970) | coding (820/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter | |||||
| * | ? | NC_008463 | = 3341157 | 478 (0.950) | 13 (0.030) | 12/266 | 36.9 | 3.1% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 397 (0.890) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 4056257 | 394 (0.780) | 12 (0.030) | 11/258 | 37.0 | 3.1% | coding (935/2262 nt) | PA14_RS18515 | chemotaxis protein CheA |
| ? | NC_008463 | 4056561 = | 406 (0.940) | coding (631/2262 nt) | PA14_RS18515 | chemotaxis protein CheA | |||||