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 51 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 | 51.7% | 513.4 / inf | 705 | intergenic (‑174/+23) | PA14_RS28345/PA14_RS28350 | type VI secretion system tip protein VgrG/Hcp family type VI secretion system effector |
| * | NC_008463 | 1,468,943 | 0 | C | T | 48.5% | 88.5 / inf | 460 | A340V (GCC→GTC) | ispC | 1‑deoxy‑D‑xylulose‑5‑phosphate reductoisomerase |
| * | NC_008463 | 5,536,163 | 0 | G | A | 47.0% | 356.2 / inf | 385 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 43.1% | 1033.1 / inf | 834 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,029,926 | 0 | A | . | 41.9% | 773.2 / inf | 311 | coding (626/1269 nt) | wecC | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| * | NC_008463 | 4,616,454 | 0 | T | G | 34.6% | 270.2 / 27.1 | 161 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 32.8% | 634.0 / inf | 516 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 32.1% | 1629.4 / inf | 745 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,039 | 0 | A | G | 30.7% | 981.3 / inf | 534 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 30.5% | 254.3 / 11.7 | 161 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 30.2% | 943.2 / inf | 506 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,584 | 0 | T | G | 30.2% | 219.7 / 16.8 | 192 | W30G (TGG→GGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 29.1% | 949.1 / 101.9 | 388 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 4,347,580 | 0 | T | G | 28.3% | 704.0 / 28.7 | 348 | intergenic (‑79/+150) | PA14_RS19855/PA14_RS19860 | hypothetical protein/zonular occludens toxin family protein |
| * | NC_008463 | 867,378 | 0 | A | C | 28.0% | 631.8 / 31.0 | 337 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.1% | 429.1 / 32.3 | 305 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 2,954,003 | 0 | T | G | 26.2% | 855.8 / 44.9 | 375 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 25.4% | 676.8 / 27.9 | 282 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 790,157 | 0 | A | C | 24.7% | 1380.3 / 78.5 | 532 | E46A (GAG→GCG) | pchF | pyochelin non‑ribosomal peptide synthetase PchF |
| * | NC_008463 | 3,515,876 | 0 | T | A | 24.6% | 606.1 / 66.2 | 287 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| Marginal new junction evidence (lowest skew 10 of 314 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 998417 | 387 (0.790) | 141 (0.290) | 100/298 | 11.2 | 26.8% | coding (1286/1884 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| ? | NC_008463 | 998421 = | 387 (0.790) | coding (1282/1884 nt) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase | |||||
| * | ? | NC_008463 | 5975365 = | 505 (1.030) | 34 (0.070) | 29/286 | 28.1 | 6.5% | coding (528/627 nt) | PA14_RS27305 | SCP2 domain‑containing protein |
| ? | NC_008463 | = 5975358 | 489 (1.040) | coding (521/627 nt) | PA14_RS27305 | SCP2 domain‑containing protein | |||||
| * | ? | NC_008463 | = 5935541 | 480 (0.980) | 23 (0.050) | 23/258 | 28.8 | 5.1% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 445 (1.050) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473569 | 603 (1.230) | 22 (0.050) | 17/288 | 33.8 | 3.6% | coding (4706/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474011 = | 601 (1.270) | coding (5148/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 3304506 | 468 (0.950) | 13 (0.030) | 13/268 | 34.8 | 3.0% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 426 (0.970) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 4523618 | 530 (1.080) | 10 (0.020) | 10/272 | 37.1 | 2.1% | coding (27/474 nt) | PA14_RS20680 | YchJ family protein |
| ? | NC_008463 | 4524021 = | 433 (0.970) | coding (430/474 nt) | PA14_RS20680 | YchJ family protein | |||||
| * | ? | NC_008463 | = 1707447 | 533 (1.080) | 10 (0.020) | 10/272 | 37.1 | 2.1% | coding (830/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein |
| ? | NC_008463 | 1707841 = | 436 (0.980) | coding (1224/1758 nt) | PA14_RS07935 | DUF1302 domain‑containing protein | |||||
| * | ? | NC_008463 | = 1458816 | 533 (1.080) | 10 (0.020) | 10/278 | 37.4 | 2.0% | coding (360/1209 nt) | dapC | succinyldiaminopimelate transaminase |
| ? | NC_008463 | 1459113 = | 467 (1.030) | coding (63/1209 nt) | dapC | succinyldiaminopimelate transaminase | |||||
| * | ? | NC_008463 | = 2341663 | 415 (0.840) | 9 (0.020) | 9/274 | 37.9 | 2.2% | pseudogene (623/957 nt) | PA14_RS10890 | DUF58 domain‑containing protein |
| ? | NC_008463 | 2341977 = | 425 (0.950) | pseudogene (937/957 nt) | PA14_RS10890 | DUF58 domain‑containing protein | |||||
| * | ? | NC_008463 | = 804437 | 465 (0.950) | 9 (0.020) | 9/274 | 37.9 | 2.0% | coding (477/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter |
| ? | NC_008463 | 804780 = | 450 (1.000) | coding (820/1245 nt) | PA14_RS03805 | RhtX/FptX family siderophore transporter | |||||