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 55 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_008463 | 933,109 | 0 | A | C | 70.4% | 562.2 / inf | 426 | V239G (GTC→GGC) | PA14_RS04350 | class C beta‑lactamase PDC‑34 |
| * | NC_008463 | 6,206,069 | 0 | T | G | 48.6% | 664.1 / inf | 745 | 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 | 48.2% | 323.4 / inf | 391 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 44.0% | 666.6 / inf | 764 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,450 | 0 | T | G | 33.8% | 271.7 / 25.6 | 172 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 33.5% | 869.9 / inf | 534 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 31.9% | 1307.5 / inf | 690 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,116,391 | 0 | C | T | 31.8% | 708.3 / inf | 574 | R504H (CGC→CAC) | ftsI | peptidoglycan D,D‑transpeptidase FtsI |
| * | NC_008463 | 5,461,135 | 0 | A | G | 31.3% | 742.5 / inf | 528 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 31.1% | 862.5 / inf | 490 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 30.9% | 337.5 / 14.2 | 164 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 29.0% | 676.4 / 32.1 | 299 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 3,515,876 | 0 | T | A | 28.7% | 594.8 / 63.1 | 293 | intergenic (+630/+254) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.6% | 414.0 / 21.9 | 281 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 26.6% | 971.3 / 90.6 | 368 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 2,954,003 | 0 | T | G | 26.4% | 939.1 / 44.7 | 406 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 2,621,464 | 0 | A | T | 25.0% | 927.0 / 72.9 | 421 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 3,515,864 | 0 | T | A | 24.8% | 539.2 / 28.2 | 284 | intergenic (+618/+266) | PA14_RS16005/PA14_RS16010 | AAA family ATPase/DUF4354 family protein |
| * | NC_008463 | 6,206,227 | 0 | G | A | 24.2% | 122.9 / 55.5 | 66 | H128H (CAC→CAT) | PA14_RS28350 | Hcp family type VI secretion system effector |
| * | NC_008463 | 5,460,283 | 0 | A | G | 24.2% | 1081.6 / inf | 454 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| Marginal new junction evidence (lowest skew 10 of 387 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 473590 | 593 (1.220) | 25 (0.060) | 24/258 | 25.8 | 4.6% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 529 (1.250) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5935541 | 519 (1.060) | 21 (0.050) | 19/256 | 28.0 | 4.6% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 426 (1.020) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 3257285 | 515 (1.060) | 13 (0.030) | 13/264 | 31.8 | 2.6% | coding (494/2055 nt) | malQ | 4‑alpha‑glucanotransferase |
| ? | NC_008463 | 3257772 = | 504 (1.170) | coding (981/2055 nt) | malQ | 4‑alpha‑glucanotransferase | |||||
| * | ? | NC_008463 | = 4056257 | 428 (0.880) | 12 (0.030) | 12/258 | 32.0 | 2.9% | coding (935/2262 nt) | PA14_RS18515 | chemotaxis protein CheA |
| ? | NC_008463 | 4056561 = | 432 (1.020) | coding (631/2262 nt) | PA14_RS18515 | chemotaxis protein CheA | |||||
| * | ? | NC_008463 | = 3395117 | 474 (0.970) | 13 (0.030) | 12/266 | 32.6 | 3.1% | coding (1131/1356 nt) | PA14_RS15470 | hypothetical protein |
| ? | NC_008463 | 3395557 = | 378 (0.870) | coding (157/261 nt) | yidD | membrane protein insertion efficiency factor YidD | |||||
| * | ? | NC_008463 | = 1030406 | 682 (1.400) | 11 (0.030) | 11/256 | 32.6 | 2.0% | coding (718/1740 nt) | PA14_RS04810 | C13 family peptidase |
| ? | NC_008463 | 1030887 = | 495 (1.180) | coding (237/1740 nt) | PA14_RS04810 | C13 family peptidase | |||||
| * | ? | NC_008463 | = 6439354 | 520 (1.070) | 11 (0.030) | 11/258 | 32.7 | 2.4% | coding (973/1290 nt) | PA14_RS29425 | MFS transporter |
| ? | NC_008463 | 6439844 = | 447 (1.060) | coding (483/1290 nt) | PA14_RS29425 | MFS transporter | |||||
| * | ? | NC_008463 | = 2377014 | 543 (1.110) | 13 (0.030) | 12/268 | 32.7 | 2.8% | coding (684/972 nt) | PA14_RS11075 | LysR family transcriptional regulator |
| ? | NC_008463 | 2377471 = | 416 (0.950) | coding (227/972 nt) | PA14_RS11075 | LysR family transcriptional regulator | |||||
| * | ? | NC_008463 | = 4693803 | 594 (1.220) | 12 (0.030) | 12/278 | 33.3 | 2.2% | coding (399/2196 nt) | PA14_RS21560 | FUSC family protein |
| ? | NC_008463 | 4694371 = | 506 (1.110) | coding (967/2196 nt) | PA14_RS21560 | FUSC family protein | |||||
| * | ? | NC_008463 | = 2936125 | 392 (0.800) | 8 (0.020) | 8/238 | 33.5 | 2.4% | noncoding (209/1289 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2936666 = | 328 (0.840) | noncoding (750/1289 nt) | CRISPR | repeat region | |||||