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 35 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 | 49.0% | 690.6 / inf | 753 | 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 | 42.4% | 459.9 / inf | 392 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 4,616,450 | 0 | T | G | 41.4% | 221.0 / 32.5 | 164 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 114,794 | 0 | A | G | 41.3% | 1069.1 / inf | 765 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.2% | 638.1 / inf | 546 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.4% | 965.4 / inf | 536 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 32.3% | 314.6 / 37.9 | 169 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 31.2% | 631.0 / 47.6 | 312 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 114,865 | 0 | T | C | 30.6% | 1624.1 / inf | 707 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,009 | 0 | A | G | 30.5% | 917.6 / inf | 508 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 28.9% | 396.8 / 25.8 | 290 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,616,448 | 0 | G | C | 28.1% | 291.8 / 40.9 | 160 | intergenic (‑168/+34) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 6,352,993 | 0 | A | T | 27.3% | 896.2 / 81.6 | 405 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 26.0% | 259.6 / 33.4 | 154 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 867,378 | 0 | A | C | 25.8% | 816.5 / 27.4 | 395 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| * | NC_008463 | 4,829,315 | 0 | T | G | 25.8% | 1053.3 / 116.8 | 415 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 4,590,213 | 0 | T | C | 25.8% | 1339.0 / inf | 520 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| * | NC_008463 | 5,125,799 | 0 | T | G | 24.8% | 376.7 / 21.6 | 232 | 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 | 23.5% | 918.6 / 19.0 | 353 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 4,616,476 | 0 | G | C | 23.1% | 338.1 / 46.5 | 156 | intergenic (‑196/+6) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 274 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 2996234 | 362 (0.740) | 35 (0.070) | 32/288 | 26.1 | 7.9% | coding (852/1635 nt) | pvdP | pyoverdine maturation tyrosinase PvdP |
| ? | NC_008463 | 3087156 = | 474 (1.010) | coding (784/888 nt) | PA14_RS14145 | TauD/TfdA family dioxygenase | |||||
| * | ? | NC_008463 | = 473590 | 688 (1.400) | 20 (0.050) | 19/260 | 29.9 | 3.5% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 494 (1.160) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5935541 | 508 (1.040) | 16 (0.040) | 15/258 | 31.8 | 3.7% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 388 (0.920) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 3304506 | 461 (0.940) | 15 (0.030) | 14/268 | 33.0 | 3.7% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 363 (0.830) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 4837368 | 545 (1.110) | 10 (0.020) | 10/272 | 35.8 | 2.1% | coding (787/1518 nt) | PA14_RS22205 | tripartite tricarboxylate transporter permease |
| ? | NC_008463 | 4837858 = | 451 (1.010) | coding (1277/1518 nt) | PA14_RS22205 | tripartite tricarboxylate transporter permease | |||||
| * | ? | NC_008463 | = 2472372 | 484 (0.990) | 9 (0.020) | 9/266 | 36.1 | 2.0% | coding (896/2379 nt) | pheT | phenylalanine‑‑tRNA ligase subunit beta |
| ? | NC_008463 | 2472706 = | 460 (1.060) | coding (1230/2379 nt) | pheT | phenylalanine‑‑tRNA ligase subunit beta | |||||
| * | ? | NC_008463 | = 2377014 | 489 (1.000) | 9 (0.020) | 9/270 | 36.4 | 2.1% | coding (684/972 nt) | PA14_RS11075 | LysR family transcriptional regulator |
| ? | NC_008463 | 2377471 = | 390 (0.880) | coding (227/972 nt) | PA14_RS11075 | LysR family transcriptional regulator | |||||
| * | ? | NC_008463 | = 213977 | 485 (0.990) | 9 (0.020) | 9/272 | 36.5 | 1.9% | coding (87/726 nt) | PA14_RS00960 | phosphatase PAP2 family protein |
| ? | NC_008463 | 214515 = | 506 (1.140) | coding (625/726 nt) | PA14_RS00960 | phosphatase PAP2 family protein | |||||
| * | ? | NC_008463 | = 2085818 | 488 (0.990) | 10 (0.020) | 9/280 | 36.9 | 2.3% | coding (951/1509 nt) | xcpR | GspE family T2SS ATPase variant XcpR |
| ? | NC_008463 | 2086152 = | 407 (0.890) | coding (1285/1509 nt) | xcpR | GspE family T2SS ATPase variant XcpR | |||||
| * | ? | NC_008463 | = 3341157 | 444 (0.900) | 8 (0.020) | 8/268 | 37.0 | 2.2% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 314 (0.720) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||