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 39 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 5,536,163 | 0 | G | A | 49.8% | 337.7 / inf | 448 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 48.7% | 628.9 / inf | 729 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 114,794 | 0 | A | G | 44.6% | 925.6 / inf | 838 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,039 | 0 | A | G | 39.4% | 695.5 / inf | 512 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 34.3% | 761.9 / inf | 461 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.0% | 627.1 / inf | 590 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 32.8% | 1580.9 / inf | 756 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 31.4% | 316.2 / 25.3 | 161 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 27.5% | 325.6 / 14.2 | 167 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 2,954,003 | 0 | T | G | 25.7% | 845.7 / 54.9 | 376 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 24.8% | 712.6 / 35.7 | 308 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 5,460,283 | 0 | A | G | 23.6% | 1039.8 / 282.4 | 432 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,590,213 | 0 | T | C | 23.3% | 1419.2 / inf | 516 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| * | NC_008463 | 4,616,448 | 0 | G | C | 22.8% | 362.1 / 33.5 | 164 | intergenic (‑168/+34) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 22.8% | 363.8 / 15.6 | 206 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 1,763,534 | 0 | T | G | 22.8% | 395.9 / 16.8 | 259 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 3,515,864 | 0 | T | A | 22.6% | 624.9 / 37.3 | 295 | intergenic (+618/+266) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 5,248,950 | 0 | T | G | 22.4% | 882.1 / 10.8 | 351 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 2,621,464 | 0 | A | T | 22.4% | 913.7 / 71.9 | 403 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 6,352,993 | 0 | A | T | 22.2% | 1089.6 / 74.3 | 434 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| Marginal new junction evidence (lowest skew 10 of 504 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 482 (0.950) | 35 (0.080) | 31/258 | 23.5 | 7.9% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 407 (0.940) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 729560 | 471 (0.930) | 39 (0.080) | 32/298 | 25.6 | 7.7% | coding (157/1092 nt) | PA14_RS03435 | anhydro‑N‑acetylmuramic acid kinase |
| ? | NC_008463 | 729571 = | 462 (0.920) | coding (146/1092 nt) | PA14_RS03435 | anhydro‑N‑acetylmuramic acid kinase | |||||
| * | ? | NC_008463 | = 229722 | 466 (0.920) | 22 (0.050) | 22/270 | 28.0 | 4.6% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 488 (1.070) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 729041 | 527 (1.040) | 30 (0.060) | 22/300 | 29.8 | 5.3% | coding (676/1092 nt) | PA14_RS03435 | anhydro‑N‑acetylmuramic acid kinase |
| ? | NC_008463 | 729055 = | 536 (1.060) | coding (662/1092 nt) | PA14_RS03435 | anhydro‑N‑acetylmuramic acid kinase | |||||
| * | ? | NC_008463 | = 473590 | 623 (1.230) | 19 (0.040) | 17/260 | 29.8 | 3.4% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 548 (1.250) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 6439354 | 561 (1.110) | 18 (0.040) | 16/260 | 30.4 | 3.7% | coding (973/1290 nt) | PA14_RS29425 | MFS transporter |
| ? | NC_008463 | 6439844 = | 445 (1.020) | coding (483/1290 nt) | PA14_RS29425 | MFS transporter | |||||
| * | ? | NC_008463 | = 3304506 | 479 (0.950) | 15 (0.030) | 15/268 | 31.5 | 3.4% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 417 (0.920) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 3143295 | 468 (0.930) | 15 (0.030) | 14/268 | 32.0 | 3.4% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 443 (0.980) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||
| * | ? | NC_008463 | = 1530568 | 687 (1.360) | 15 (0.030) | 14/272 | 32.3 | 2.7% | coding (1099/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein |
| ? | NC_008463 | 1531091 = | 455 (0.990) | coding (1622/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 419388 | 492 (0.970) | 14 (0.030) | 13/278 | 33.3 | 2.8% | coding (1484/1734 nt) | ggt | gamma‑glutamyltransferase |
| ? | NC_008463 | 419804 = | 503 (1.070) | coding (1068/1734 nt) | ggt | gamma‑glutamyltransferase | |||||