mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 48 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 | 51.0% | 591.5 / inf | 770 | 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 | 49.5% | 309.3 / inf | 414 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 40.5% | 1200.1 / inf | 851 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 39.6% | 248.3 / 30.8 | 158 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 37.0% | 476.1 / inf | 514 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 37.0% | 256.9 / 23.3 | 171 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 34.1% | 908.8 / inf | 571 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 33.5% | 878.9 / inf | 541 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 32.2% | 544.9 / 58.6 | 295 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 114,865 | 0 | T | C | 30.7% | 1715.1 / inf | 754 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,439 | 0 | C | G | 29.9% | 235.9 / 56.3 | 157 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 26.6% | 421.3 / 29.9 | 283 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 6,206,227 | 0 | G | A | 25.7% | 137.8 / 62.4 | 71 | H128H (CAC→CAT) | PA14_RS28350 | Hcp family type VI secretion system effector |
| * | NC_008463 | 2,621,464 | 0 | A | T | 25.4% | 1007.9 / 86.7 | 476 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 5,248,950 | 0 | T | G | 25.2% | 925.8 / 22.1 | 354 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 2,954,003 | 0 | T | G | 25.2% | 1015.6 / 36.7 | 428 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 24.7% | 663.9 / 49.0 | 286 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 5,460,283 | 0 | A | G | 24.6% | 1114.9 / inf | 481 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,457 | 0 | C | G | 24.5% | 297.1 / 32.6 | 159 | intergenic (‑177/+25) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 3,630,825 | 0 | G | T | 24.2% | 370.6 / 30.2 | 213 | intergenic (+16/‑259) | tse1/metH | type VI secretion system effector peptidoglycanhydrolase Tse1/methionine synthase |
| Marginal new junction evidence (lowest skew 10 of 261 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 473590 | 658 (1.290) | 23 (0.050) | 21/260 | 28.4 | 4.1% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 512 (1.160) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 1530568 | 614 (1.200) | 14 (0.030) | 12/272 | 34.1 | 2.7% | coding (1099/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein |
| ? | NC_008463 | 1531091 = | 460 (1.000) | coding (1622/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 229722 | 550 (1.080) | 11 (0.020) | 11/270 | 34.6 | 2.2% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 499 (1.090) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 5884344 | 529 (1.040) | 11 (0.020) | 11/274 | 34.9 | 2.0% | 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 = | 610 (1.310) | 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 | = 5935541 | 504 (0.990) | 10 (0.020) | 9/258 | 35.3 | 2.2% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 465 (1.060) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 270317 | 504 (0.990) | 9 (0.020) | 9/272 | 36.2 | 1.8% | coding (244/1185 nt) | pobA | 4‑hydroxybenzoate 3‑monooxygenase |
| ? | NC_008463 | 270615 = | 520 (1.130) | intergenic (‑55/‑123) | pobA/PA14_RS01225 | 4‑hydroxybenzoate 3‑monooxygenase/helix‑turn‑helix domain‑containing protein | |||||
| * | ? | NC_008463 | = 5422623 | 548 (1.080) | 10 (0.020) | 9/278 | 36.5 | 2.0% | coding (919/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ |
| ? | NC_008463 | 5423053 = | 480 (1.020) | coding (489/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ | |||||
| * | ? | NC_008463 | = 992802 | 565 (1.110) | 9 (0.020) | 9/278 | 36.5 | 1.6% | coding (445/480 nt) | nusB | transcription antitermination factor NusB |
| ? | NC_008463 | 993104 = | 615 (1.300) | coding (249/969 nt) | thiL | thiamine‑phosphate kinase | |||||
| * | ? | NC_008463 | = 3304506 | 467 (0.920) | 8 (0.020) | 8/268 | 36.7 | 1.9% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 405 (0.890) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 44749 | 597 (1.170) | 8 (0.020) | 8/268 | 36.7 | 1.8% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 347 (0.760) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||