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 | 5,541,242 | 0 | T | C | 68.6% | 85.9 / inf | 294 | intergenic (‑50/+493) | PA14_RS25375/msrQ | 16S ribosomal RNA/protein‑methionine‑sulfoxide reductase heme‑binding subunit MsrQ |
| * | NC_008463 | 2,028,729 | 0 | C | T | 68.4% | 746.3 / inf | 380 | R216C (CGC→TGC) | wecB | UDP‑N‑acetylglucosamine 2‑epimerase (non‑hydrolyzing) |
| * | NC_008463 | 6,206,069 | 0 | T | G | 50.3% | 574.9 / inf | 721 | 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 | 42.9% | 468.4 / inf | 411 | intergenic (‑12/+132) | rrf/PA14_RS25360 | 5S ribosomal RNA/23S ribosomal RNA |
| * | NC_008463 | 114,794 | 0 | A | G | 38.8% | 1324.6 / inf | 847 | K505R (AAG→AGG) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 5,461,135 | 0 | A | G | 35.0% | 649.4 / inf | 606 | D1240D (GAT→GAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,039 | 0 | A | G | 32.6% | 967.6 / inf | 561 | G1272G (GGT→GGC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 5,461,009 | 0 | A | G | 32.3% | 836.0 / inf | 496 | N1282N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 4,829,315 | 0 | T | G | 29.9% | 968.2 / 128.9 | 408 | K8T (AAA→ACA) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 114,865 | 0 | T | C | 26.9% | 1965.4 / inf | 771 | Y529H (TAC→CAC) | vgrG1b | type VI secretion system spike protein VgrG1b |
| * | NC_008463 | 4,616,476 | 0 | G | C | 26.1% | 273.0 / 43.9 | 138 | intergenic (‑196/+6) | hda/PA14_RS21180 | DnaA regulatory inactivator Hda/DUF2066 domain‑containing protein |
| * | NC_008463 | 5,910,256 | 0 | A | C | 25.9% | 740.4 / 42.4 | 302 | intergenic (+55/‑90) | aceE/aceF | pyruvate dehydrogenase (acetyl‑transferring), homodimeric type/dihydrolipoyllysine‑residue acetyltransferase |
| * | NC_008463 | 1,763,534 | 0 | T | G | 25.0% | 529.8 / 23.1 | 326 | L13R (CTC→CGC) | PA14_RS08240 | RHS repeat protein |
| * | NC_008463 | 6,352,993 | 0 | A | T | 24.6% | 990.8 / 60.2 | 413 | intergenic (+73/‑46) | dgcB/PA14_RS29035 | dimethylglycine demethylation protein DgcB/electron transfer flavoprotein subunit alpha/FixB family protein |
| * | NC_008463 | 5,125,799 | 0 | T | G | 24.3% | 430.9 / 21.7 | 244 | intergenic (‑54/+32) | PA14_RS23455/PA14_RS23460 | glutathione S‑transferase N‑terminal domain‑containing protein/cytochrome c1 |
| * | NC_008463 | 2,954,003 | 0 | T | G | 24.0% | 966.5 / 34.2 | 398 | Q75P (CAG→CCG) | PA14_RS13685 | DUF6162 family protein |
| * | NC_008463 | 5,460,283 | 0 | A | G | 23.6% | 1216.3 / inf | 519 | N1524N (AAT→AAC) | PA14_RS25000 | MBG domain‑containing protein |
| * | NC_008463 | 6,224,310 | 0 | A | C | 22.9% | 1047.9 / 24.8 | 374 | intergenic (‑242/+19) | PA14_RS28445/PA14_RS28450 | secondary thiamine‑phosphate synthase enzyme YjbQ/ammonium transporter |
| * | NC_008463 | 4,829,317 | 0 | C | G | 22.8% | 1074.2 / 64.8 | 418 | L7L (CTG→CTC) | PA14_RS22165 | succinate dehydrogenase assembly factor 2 |
| * | NC_008463 | 867,378 | 0 | A | C | 22.8% | 880.8 / 19.7 | 404 | L390R (CTG→CGG) | PA14_RS04080 | MFS transporter |
| Marginal new junction evidence (lowest skew 10 of 380 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_008463 | = 5935541 | 547 (1.070) | 29 (0.070) | 26/258 | 25.9 | 5.8% | coding (251/981 nt) | PA14_RS27150 | hypothetical protein |
| ? | NC_008463 | 5935938 = | 472 (1.070) | coding (648/981 nt) | PA14_RS27150 | hypothetical protein | |||||
| * | ? | NC_008463 | = 2042839 | 315 (0.720) | 76 (0.160) +GCGGTGCAGGCC |
16/232 | 28.9 | 17.9% | coding (1230/1998 nt) | PA14_RS09500 | nucleoside‑diphosphate sugar epimerase/dehydratase |
| ? | NC_008463 | 2042840 = | 389 (0.760) | coding (1231/1998 nt) | PA14_RS09500 | nucleoside‑diphosphate sugar epimerase/dehydratase | |||||
| * | ? | NC_008463 | 5251438 = | 303 (0.590) | 12 (0.030) | 11/208 | 30.1 | 5.0% | intergenic (+231/+1) | tpsA4/PA14_RS31290 | two‑partner secretion system exoprotein TpsA4/tRNA‑Lys |
| ? | NC_008463 | = 5359391 | 248 (0.700) | intergenic (+367/+2) | PA14_RS24540/PA14_RS24545 | site‑specific integrase/tRNA‑Lys | |||||
| * | ? | NC_008463 | = 229722 | 557 (1.090) | 20 (0.040) | 18/270 | 30.4 | 4.1% | coding (676/882 nt) | PA14_RS01030 | triphosphoribosyl‑dephospho‑CoA synthase |
| ? | NC_008463 | 230146 = | 440 (0.960) | coding (217/300 nt) | PA14_RS01035 | malonate decarboxylase subunit delta | |||||
| * | ? | NC_008463 | = 46919 | NA (NA) | 14 (0.030) | 14/276 | 33.0 | 100% | coding (3986/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 47235 = | 0 (0.000) | coding (4302/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 | |||||
| * | ? | NC_008463 | = 3341157 | 499 (0.980) | 14 (0.030) | 13/268 | 33.1 | 3.1% | coding (217/510 nt) | PA14_RS15275 | aromatic‑ring‑hydroxylating dioxygenase subunit beta |
| ? | NC_008463 | 3341605 = | 423 (0.930) | coding (1629/1833 nt) | asnB | asparagine synthase (glutamine‑hydrolyzing) | |||||
| * | ? | NC_008463 | = 3143295 | 487 (0.950) | 15 (0.030) | 13/268 | 33.1 | 3.4% | coding (731/783 nt) | PA14_RS14385 | TIM barrel protein |
| ? | NC_008463 | 3143692 = | 430 (0.940) | coding (334/783 nt) | PA14_RS14385 | TIM barrel protein | |||||
| * | ? | NC_008463 | = 1030391 | 628 (1.230) | 12 (0.030) | 12/262 | 33.4 | 2.2% | coding (733/1740 nt) | PA14_RS04810 | C13 family peptidase |
| ? | NC_008463 | 1030737 = | 527 (1.180) | coding (387/1740 nt) | PA14_RS04810 | C13 family peptidase | |||||
| * | ? | NC_008463 | = 3304506 | 429 (0.840) | 12 (0.030) | 11/268 | 34.4 | 2.9% | coding (1023/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein |
| ? | NC_008463 | 3304825 = | 410 (0.900) | coding (704/1449 nt) | PA14_RS15105 | aldehyde dehydrogenase family protein | |||||
| * | ? | NC_008463 | = 44749 | 681 (1.330) | 13 (0.030) | 11/268 | 34.4 | 2.7% | coding (1816/10332 nt) | tpsA2 | two‑partner secretion system putative hemagglutinin TpsA2 |
| ? | NC_008463 | 2855205 = | 343 (0.750) | coding (6638/15639 nt) | PA14_RS13370 | hemagglutinin repeat‑containing protein | |||||