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 34 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 | 48.4% | 661.3 / inf | 744 | 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 | 45.9% | 399.5 / inf | 425 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 39.1% | 1225.6 / inf | 810 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,450 | 0 | T | G | 33.9% | 220.1 / 15.8 | 144 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 33.8% | 859.2 / inf | 507 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 33.6% | 562.8 / inf | 517 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,454 | 0 | T | G | 32.4% | 246.1 / 27.8 | 139 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 31.4% | 841.1 / inf | 475 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 29.6% | 1733.5 / inf | 738 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 2,954,003 | 0 | T | G | 27.3% | 906.3 / 52.6 | 403 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 4,616,439 | 0 | C | G | 26.9% | 221.7 / 41.1 | 134 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 24.5% | 692.3 / 28.0 | 302 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 1,763,534 | 0 | T | G | 24.4% | 474.3 / 20.4 | 316 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 24.3% | 1050.3 / 88.0 | 382 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 5,248,950 | 0 | T | G | 24.2% | 898.0 / 16.0 | 364 | L666R (CTG→CGG) | tpsA4 | two‑partner secretion system exoprotein TpsA4 |
| * | NC_008463 | 5,460,283 | 0 | A | G | 24.1% | 1169.5 / inf | 509 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,590,213 | 0 | T | C | 23.3% | 1516.9 / inf | 554 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| * | NC_008463 | 2,941,693 | 0 | T | G | 23.1% | 732.2 / 18.3 | 300 | intergenic (‑64/+34) | PA14_RS13620/PA14_RS13625 | hydrolase/pirin family protein |
| * | NC_008463 | 5,460,364 | 0 | A | G | 23.0% | 907.6 / 239.3 | 404 | Y1497Y (TAT→TAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 790,157 | 0 | A | C | 22.9% | 1487.9 / 58.0 | 553 | E46A (GAG→GCG) | pchF | pyochelin non‑ribosomal peptide synthetase PchF |
| Marginal new junction evidence (lowest skew 10 of 506 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 503 (0.980) | 26 (0.060) | 23/258 | 26.6 | 5.7% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 434 (0.980) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 473590 | 662 (1.290) | 21 (0.050) | 20/260 | 28.2 | 3.6% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 539 (1.210) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 5251483 | 304 (0.590) | 12 (0.030) | 9/208 | 30.9 | 5.2% | noncoding (78/122 nt) | PA14_RS31290 | tRNA‑Lys |
| ? | NC_008463 | 5359438 = | 223 (0.630) | noncoding (31/76 nt) | PA14_RS24545 | tRNA‑Lys | |||||
| * | ? | NC_008463 | = 3341157 | 506 (0.990) | 17 (0.040) | 15/268 | 31.3 | 4.0% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 371 (0.810) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 44749 | 624 (1.220) | 14 (0.030) | 14/268 | 31.9 | 2.9% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 389 (0.850) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||
| * | ? | NC_008463 | = 44749 | 624 (1.220) | 14 (0.030) | 14/268 | 31.9 | 2.8% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 45182 = | 419 (0.920) | coding (2249/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 1571119 | 421 (0.820) | 15 (0.030) | 14/274 | 32.2 | 3.3% | coding (131/414 nt) | arnF | 4‑amino‑4‑deoxy‑L‑arabinose‑phosphoundecaprenol flippase subunit ArnF |
| ? | NC_008463 | 1571590 = | 506 (1.080) | coding (4/348 nt) coding (1650/1650 nt) |
PA14_RS07350 arnT |
EamA family transporter lipid IV(A) 4‑amino‑4‑deoxy‑L‑arabinosyltransferase |
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| * | ? | NC_008463 | = 5422623 | 598 (1.170) | 14 (0.030) | 14/278 | 32.5 | 2.6% | coding (919/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ |
| ? | NC_008463 | 5423053 = | 499 (1.050) | coding (489/1440 nt) | oprJ | multidrug efflux transporter outer membrane subunit OprJ | |||||
| * | ? | NC_008463 | = 3143295 | 535 (1.040) | 14 (0.030) | 13/268 | 32.5 | 2.8% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 489 (1.070) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||
| * | ? | NC_008463 | = 2926608 | 452 (0.880) | 9 (0.020) | 9/230 | 32.6 | 2.5% | noncoding (89/874 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2927029 = | 350 (0.890) | noncoding (510/874 nt) | CRISPR | repeat region | |||||