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 41 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 5,536,163 | 0 | G | A | 52.3% | 242.6 / inf | 394 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 46.2% | 779.7 / inf | 792 | 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 | 41.8% | 831.5 / inf | 799 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 34.9% | 244.8 / 32.7 | 154 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 33.9% | 245.4 / 18.9 | 157 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.8% | 824.4 / inf | 497 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 32.4% | 641.3 / inf | 528 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 30.6% | 573.4 / 41.2 | 270 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 5,461,009 | 0 | A | G | 29.4% | 836.0 / inf | 458 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 29.2% | 250.8 / 48.2 | 154 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 29.2% | 1556.9 / inf | 741 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 1,763,534 | 0 | T | G | 28.2% | 467.8 / 29.6 | 325 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 26.4% | 331.6 / 19.9 | 219 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 2,954,003 | 0 | T | G | 26.2% | 868.5 / 49.3 | 384 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 867,378 | 0 | A | C | 25.4% | 739.5 / 19.3 | 386 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| * | NC_008463 | 4,616,448 | 0 | G | C | 25.2% | 297.7 / 36.2 | 160 | intergenic (‑168/+34) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 24.8% | 1089.6 / 90.3 | 401 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 5,248,950 | 0 | T | G | 23.4% | 971.2 / 16.5 | 361 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 3,515,876 | 0 | T | A | 23.3% | 697.7 / 52.7 | 306 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 2,621,464 | 0 | A | T | 22.9% | 840.8 / 56.9 | 390 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| Marginal new junction evidence (lowest skew 10 of 449 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 473590 | 638 (1.270) | 41 (0.090) | 35/258 | 23.7 | 7.2% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 499 (1.150) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5935541 | 506 (1.010) | 18 (0.040) | 15/256 | 32.9 | 3.9% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 450 (1.050) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 5251483 | 295 (0.590) | 8 (0.020) | 8/206 | 33.7 | 3.4% | noncoding (78/122 nt) | PA14_RS31290 | tRNA‑Lys |
| ? | NC_008463 | 5359438 = | 249 (0.720) | noncoding (31/76 nt) | PA14_RS24545 | tRNA‑Lys | |||||
| * | ? | NC_008463 | = 47641 | NA (NA) | 14 (0.030) | 13/274 | 35.4 | 100% | coding (4708/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 48224 = | 0 (0.000) | coding (5291/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 3304506 | 450 (0.900) | 13 (0.030) | 12/266 | 35.5 | 3.1% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 417 (0.930) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 515742 | 470 (0.940) | 13 (0.030) | 13/276 | 35.5 | 3.0% | coding (137/1224 nt) | PA14_RS02350 | CaiB/BaiF CoA‑transferase family protein |
| ? | NC_008463 | 516254 = | 395 (0.850) | coding (926/1182 nt) | PA14_RS02355 | acyl‑CoA dehydrogenase | |||||
| * | ? | NC_008463 | = 419388 | 511 (1.020) | 12 (0.030) | 12/276 | 36.1 | 2.5% | coding (1484/1734 nt) | ggt | gamma‑glutamyltransferase |
| ? | NC_008463 | 419804 = | 468 (1.010) | coding (1068/1734 nt) | ggt | gamma‑glutamyltransferase | |||||
| * | ? | NC_008463 | = 229722 | 474 (0.950) | 12 (0.030) | 11/268 | 36.3 | 2.6% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 478 (1.060) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 5884344 | 513 (1.030) | 11 (0.020) | 11/272 | 36.5 | 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 = | 587 (1.290) | 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 | = 872921 | 555 (1.110) | 12 (0.030) | 11/276 | 36.8 | 2.3% | coding (503/906 nt) | fepB | Fe2+‑enterobactin ABC transporter substrate‑binding protein |
| ? | NC_008463 | 873360 = | 509 (1.100) | coding (64/906 nt) | fepB | Fe2+‑enterobactin ABC transporter substrate‑binding protein | |||||