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 | 51.9% | 265.2 / inf | 423 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 6,206,069 | 0 | T | G | 49.2% | 711.6 / inf | 818 | 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 | 43.4% | 1027.3 / inf | 831 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,454 | 0 | T | G | 40.0% | 250.3 / 48.7 | 179 | intergenic (‑174/+28) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 38.2% | 862.6 / inf | 595 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,616,450 | 0 | T | G | 36.4% | 241.6 / 31.0 | 185 | intergenic (‑170/+32) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 35.5% | 847.9 / inf | 547 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 114,865 | 0 | T | C | 33.0% | 1636.2 / inf | 769 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,829,315 | 0 | T | G | 31.1% | 989.6 / 137.2 | 429 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 4,616,448 | 0 | G | C | 30.5% | 270.0 / 46.1 | 178 | intergenic (‑168/+34) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,461,135 | 0 | A | G | 28.5% | 868.2 / inf | 598 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 1,763,534 | 0 | T | G | 27.6% | 490.5 / 34.0 | 327 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 1,763,584 | 0 | T | G | 26.1% | 270.4 / 12.7 | 193 | W30G (TGG→GGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 6,352,993 | 0 | A | T | 26.0% | 964.1 / 78.4 | 410 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 25.7% | 762.4 / 31.2 | 334 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 3,688,136 | 0 | T | G | 25.6% | 845.5 / 23.0 | 295 | S168A (TCG→GCG) | folD | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| * | NC_008463 | 2,621,464 | 0 | A | T | 23.7% | 1025.5 / 75.4 | 459 | intergenic (‑9/+29) | aat/trxB | leucyl/phenylalanyl‑tRNA‑‑protein transferase/thioredoxin‑disulfide reductase |
| * | NC_008463 | 4,616,439 | 0 | C | G | 23.5% | 281.9 / 45.9 | 170 | intergenic (‑159/+43) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 1,763,540 | 0 | T | G | 23.4% | 524.6 / 11.5 | 326 | L15R (CTG→CGG) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 4,590,213 | 0 | T | C | 23.3% | 1655.8 / inf | 611 | T254T (ACT→ACC) | PA14_RS21015 | site‑specific integrase |
| Marginal new junction evidence (lowest skew 10 of 259 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 553 (1.030) | 25 (0.050) | 24/258 | 28.3 | 5.2% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 438 (0.950) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 2396078 | 308 (0.570) | 18 (0.030) | 17/290 | 33.9 | 5.3% | coding (235/321 nt) | PA14_RS11185 | RebB family R body protein |
| ? | NC_008463 | 2396459 = | 344 (0.660) | coding (237/321 nt) | PA14_RS11190 | RebB family R body protein | |||||
| * | ? | NC_008463 | = 473590 | 727 (1.350) | 14 (0.030) | 13/260 | 34.3 | 2.4% | coding (4727/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA |
| ? | NC_008463 | 474032 = | 499 (1.070) | coding (5169/7431 nt) | chpA | chemotaxis signal transduction system protein ChpA | |||||
| * | ? | NC_008463 | = 47641 | NA (NA) | 14 (0.030) | 14/276 | 34.7 | 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 | = 2926608 | 460 (0.860) | 10 (0.020) | 9/230 | 34.9 | 2.8% | noncoding (89/874 nt) | CRISPR | repeat region |
| ? | NC_008463 | 2927029 = | 351 (0.850) | noncoding (510/874 nt) | CRISPR | repeat region | |||||
| * | ? | NC_008463 | = 3304506 | 538 (1.000) | 11 (0.020) | 11/268 | 36.1 | 2.4% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 430 (0.900) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 1809504 | 525 (0.980) | 10 (0.020) | 10/278 | 37.5 | 2.1% | coding (117/1167 nt) | PA14_RS08445 | NAD(P)/FAD‑dependent oxidoreductase |
| ? | NC_008463 | 1809852 = | 425 (0.850) | coding (6824/7059 nt) | PA14_RS08450 | non‑ribosomal peptide synthetase | |||||
| * | ? | NC_008463 | = 3395117 | 476 (0.890) | 9 (0.020) | 9/268 | 37.6 | 2.1% | coding (1131/1356 nt) | PA14_RS15470 | hypothetical protein |
| ? | NC_008463 | 3395557 = | 435 (0.910) | coding (157/261 nt) | yidD | membrane protein insertion efficiency factor YidD | |||||
| * | ? | NC_008463 | = 229722 | 554 (1.030) | 9 (0.020) | 9/270 | 37.7 | 1.7% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 524 (1.080) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 1530568 | 667 (1.240) | 10 (0.020) | 9/272 | 37.8 | 1.8% | coding (1099/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein |
| ? | NC_008463 | 1531091 = | 502 (1.030) | coding (1622/1728 nt) | PA14_RS07160 | acyl‑CoA dehydrogenase family protein | |||||