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 42 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 | 49.0% | 355.8 / inf | 446 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 47.5% | 665.4 / inf | 767 | 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 | 40.9% | 919.3 / inf | 817 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,030,086 | 0 | G | . | 35.8% | 774.7 / inf | 296 | coding (786/1269 nt) | wecC | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| * | NC_008463 | 5,461,135 | 0 | A | G | 35.2% | 547.9 / inf | 524 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 35.1% | 825.3 / inf | 556 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 33.9% | 746.8 / inf | 480 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 3,515,876 | 0 | T | A | 32.8% | 536.6 / 80.0 | 297 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 114,865 | 0 | T | C | 29.1% | 1547.7 / inf | 724 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.9% | 469.4 / 26.4 | 312 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 26.9% | 323.9 / 16.1 | 157 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 2,029,586 | 0 | C | T | 26.8% | 596.4 / inf | 355 | R96* (CGA→TGA) | wecC | UDP‑N‑acetyl‑D‑mannosamine dehydrogenase |
| * | NC_008463 | 5,460,283 | 0 | A | G | 26.1% | 1182.2 / inf | 522 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 24.9% | 1094.9 / 115.0 | 431 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 3,515,878 | 0 | T | A | 24.2% | 664.9 / 50.8 | 297 | intergenic (+632/+252) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 6,206,227 | 0 | G | A | 24.1% | 164.2 / 60.1 | 79 | H128H (CAC→CAT) | PA14_RS28350 | Hcp family type VI secretion system effector |
| * | NC_008463 | 5,910,256 | 0 | A | C | 23.8% | 743.1 / 24.4 | 308 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 4,089,353 | 0 | T | A | 23.8% | 441.0 / 33.0 | 294 | intergenic (‑136/+30) | PA14_RS18660/PA14_RS18665 | cation‑transporting P‑type ATPase/acetyltransferase |
| * | NC_008463 | 6,352,993 | 0 | A | T | 23.8% | 891.8 / 72.2 | 378 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 867,378 | 0 | A | C | 23.2% | 746.0 / 24.7 | 387 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| Marginal new junction evidence (lowest skew 10 of 372 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 502 (0.990) | 26 (0.060) | 24/256 | 26.3 | 5.5% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 470 (1.080) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473590 | 595 (1.180) | 17 (0.040) | 17/258 | 29.8 | 3.3% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 495 (1.130) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 3039478 | 515 (1.020) | 16 (0.030) | 16/272 | 31.3 | 3.3% | coding (153/561 nt) | msuE | FMN reductase |
| ? | NC_008463 | 3039851 = | 472 (1.020) | coding (526/561 nt) | msuE | FMN reductase | |||||
| * | ? | NC_008463 | = 3143295 | 498 (0.980) | 15 (0.030) | 15/266 | 31.4 | 3.3% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 446 (0.990) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||
| * | ? | NC_008463 | = 704259 | 519 (1.030) | 16 (0.040) | 14/262 | 31.8 | 3.1% | coding (849/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein |
| ? | NC_008463 | 704746 = | 555 (1.250) | coding (1336/1836 nt) | PA14_RS03305 | phage tail tape measure C‑terminal domain‑containing protein | |||||
| * | ? | NC_008463 | = 3395117 | 432 (0.850) | 12 (0.030) | 11/266 | 33.9 | 3.0% | coding (1131/1356 nt) | PA14_RS15470 | hypothetical protein |
| ? | NC_008463 | 3395557 = | 380 (0.840) | coding (157/261 nt) | yidD | membrane protein insertion efficiency factor YidD | |||||
| * | ? | NC_008463 | = 911595 | 570 (1.130) | 11 (0.020) | 11/268 | 34.0 | 2.2% | coding (100/807 nt) | hpaI | 4‑hydroxy‑2‑oxoheptanedioate aldolase |
| ? | NC_008463 | 912016 = | 450 (0.990) | coding (495/804 nt) | hpaH | 2‑oxo‑hepta‑3‑ene‑1,7‑dioic acid hydratase | |||||
| * | ? | NC_008463 | = 2936784 | 497 (0.980) | 9 (0.020) | 8/240 | 34.3 | 2.3% | noncoding (868/1289 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2937146 = | 362 (0.890) | noncoding (1230/1289 nt) | CRISPR | repeat region | |||||
| * | ? | NC_008463 | = 5422623 | 513 (1.010) | 11 (0.020) | 11/276 | 34.5 | 2.4% | coding (919/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ |
| ? | NC_008463 | 5423053 = | 434 (0.930) | coding (489/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ | |||||
| * | ? | NC_008463 | = 2512529 | 486 (0.960) | 10 (0.020) | 9/272 | 35.6 | 2.2% | coding (1401/2310 nt) | PA14_RS11840 | molybdopterin oxidoreductase family protein |
| ? | NC_008463 | 2512965 = | 459 (0.990) | coding (965/2310 nt) | PA14_RS11840 | molybdopterin oxidoreductase family protein | |||||