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 | 5,388,740 | 0 | T | . | 60.2% | 288.5 / inf | 528 | coding (15/258 nt) | rpmA | 50S ribosomal protein L27 |
| * | NC_008463 | 6,206,069 | 0 | T | G | 48.5% | 659.5 / inf | 733 | 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 | 47.5% | 382.4 / inf | 439 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 42.0% | 997.1 / inf | 778 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 37.3% | 287.3 / 29.9 | 164 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.2% | 540.2 / inf | 512 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 32.9% | 279.3 / 19.9 | 163 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 32.6% | 521.1 / 41.4 | 261 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.5% | 918.7 / inf | 527 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 30.8% | 1592.6 / inf | 711 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,954,003 | 0 | T | G | 27.6% | 788.7 / 43.1 | 369 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 26.9% | 251.5 / 36.2 | 149 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 26.1% | 1065.0 / inf | 516 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 25.1% | 404.1 / 21.1 | 230 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 3,688,136 | 0 | T | G | 24.3% | 835.1 / 15.3 | 290 | S168A (TCG→GCG) | folD | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| * | NC_008463 | 3,515,876 | 0 | T | A | 23.9% | 666.7 / 44.1 | 289 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 23.8% | 1185.9 / 94.0 | 436 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 790,157 | 0 | A | C | 23.4% | 1552.8 / 61.2 | 592 | E46A (GAG→GCG) | pchF | pyochelin non‑ribosomal peptide synthetase PchF |
| * | NC_008463 | 867,378 | 0 | A | C | 23.4% | 827.0 / 21.7 | 375 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| * | NC_008463 | 2,351,469 | 0 | A | C | 22.9% | 803.7 / 27.9 | 324 | S170R (AGC→CGC) | PA14_RS10935 | transglycosylase SLT domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 460 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 519 (1.050) | 31 (0.070) | 30/258 | 23.3 | 6.4% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 467 (1.100) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473590 | 617 (1.250) | 14 (0.030) | 13/260 | 31.4 | 2.5% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 538 (1.250) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 46919 | NA (NA) | 15 (0.030) | 14/276 | 31.8 | 100% | coding (3986/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 47235 = | 0 (0.000) | coding (4302/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 3304506 | 436 (0.880) | 13 (0.030) | 13/268 | 31.9 | 3.1% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 430 (0.970) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 3341157 | 463 (0.940) | 12 (0.030) | 12/268 | 32.5 | 3.0% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 376 (0.850) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 100189 | 534 (1.080) | 11 (0.020) | 11/268 | 33.1 | 2.3% | coding (759/1497 nt) | tssC | type VI secretion system contractile sheath large subunit |
| ? | NC_008463 | 100610 = | 453 (1.020) | coding (1180/1497 nt) | tssC | type VI secretion system contractile sheath large subunit | |||||
| * | ? | NC_008463 | = 2512529 | 476 (0.960) | 11 (0.020) | 11/274 | 33.5 | 2.4% | coding (1401/2310 nt) | PA14_RS11840 | molybdopterin oxidoreductase family protein |
| ? | NC_008463 | 2512965 = | 475 (1.050) | coding (965/2310 nt) | PA14_RS11840 | molybdopterin oxidoreductase family protein | |||||
| * | ? | NC_008463 | = 419388 | 550 (1.110) | 12 (0.030) | 11/278 | 33.7 | 2.5% | coding (1484/1734 nt) | ggt | gamma‑glutamyltransferase |
| ? | NC_008463 | 419804 = | 432 (0.940) | coding (1068/1734 nt) | ggt | gamma‑glutamyltransferase | |||||
| * | ? | NC_008463 | = 2858245 | NA (NA) | 10 (0.020) | 10/280 | 34.5 | 2.8% | coding (9678/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein |
| ? | NC_008463 | 2858762 = | 373 (0.750) | coding (10195/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||
| * | ? | NC_008463 | = 4733882 | 394 (0.800) | 9 (0.020) | 9/272 | 34.7 | 2.1% | coding (807/1221 nt) | PA14_RS21730 | glycosyltransferase family 1 protein |
| ? | NC_008463 | 4734438 = | 500 (1.110) | coding (822/960 nt) | PA14_RS21735 | DegV family protein | |||||