mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 451,643 | G→A | 76.7% | intergenic (‑33/+427) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 652,453 | G→A | 5.4% | A73A (GCG→GCA) | citA → | sensory histidine kinase in two‑component regulatory system with CitB |
| RA | 779,226 | Δ1 bp | 4.4% | coding (160/522 nt) | pal → | peptidoglycan‑associated outer membrane lipoprotein |
| RA | 970,421 | C→T | 4.9% | R345C (CGC→TGC) | ycaQ → | DUF1006 family protein with C‑terminal wHTH domain |
| RA | 989,521 | C→A | 4.4% | G279V (GGC→GTC) | pncB ← | nicotinate phosphoribosyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,708,662 | C→G | 6.9% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 14.1% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,847 | G→A | 11.4% | E643E (GAG→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,902,141 | G→A | 5.2% | G32S (GGC→AGC) | manX → | fused mannose‑specific PTS enzymes: IIA component/IIB component |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,202,094 | G→A | 8.8% | A606A (GCG→GCA) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,241,662:1 | +A | 5.1% | coding (5/1041 nt) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor |
| RA | 2,304,678 | T→C | 9.5% | intergenic (+287/+428) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,649,036 | A→C | 4.2% | F1084V (TTT→GTT) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,854,256 | A→T | 4.9% | I335I (ATA→ATT) | hypE → | carbamoyl dehydratase, hydrogenases 1,2,3 maturation protein |
| RA | 3,065,954 | A→G | 8.3% | E385E (GAA→GAG) | scpC → | propionyl‑CoA:succinate CoA transferase |
| RA | 3,339,606 | G→C | 3.2% | A153G (GCA→GGA) | mlaF ← | ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,951,535 | Δ1 bp | 100% | pseudogene (977/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,951,597:1 | +A | 6.0% | pseudogene (57/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted |
| JC | 3,968,507 | Δ12 bp | 10.8% | coding (593‑604/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| JC | 3,968,670 | Δ9 bp | 5.4% | coding (756‑764/1104 nt) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,012,601 | A→T | 3.2% | V72E (GTA→GAA) | metR ← | methionine biosynthesis regulon transcriptional regulator |
| RA | 4,146,260 | A→G | 3.2% | D756G (GAC→GGC) T2A (ACA→GCA) |
pflD → pflC → |
putative glycine radical domain‑containing pyruvate formate‑lyase putative [formate‑C‑acetyltransferase 2]‑activating enzyme, pyruvate formate‑lyase 1‑activating enzyme |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,274,207 | C→T | 3.7% | G28G (GGC→GGT) | ssb → | single‑stranded DNA‑binding protein |
| RA | 4,296,189 | A→G | 34.1% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 45.0% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 9.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,544,445 | T→C | 9.3% | Y47Y (TAT→TAC) | fimC → | periplasmic chaperone |
| RA | 4,565,628 | C→T | 4.6% | R75H (CGC→CAC) | yjiM ← | putative 2‑hydroxyglutaryl‑CoA dehydratase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2469042 | 2469912 | 871 | 23 [21] | [21] 22 | [gtrB]–[gtrS] | [gtrB], [gtrS] |
| * | * | ÷ | NC_000913 | 2785996 | 2786710 | 715 | 22 [20] | [21] 23 | [ygaQ] | [ygaQ] |
| * | * | ÷ | NC_000913 | 2994959 | 2995475 | 517 | 23 [21] | [20] 25 | [ygeK]–[ygeN] | [ygeK], [ygeN] |
| * | * | ÷ | NC_000913 | 3287074 | 3287427 | 354 | 23 [21] | [19] 23 | [yraH] | [yraH] |
| * | * | ÷ | NC_000913 | 3360767 | 3361277 | 511 | 23 [21] | [21] 23 | [gltF] | [gltF] |
| * | * | ÷ | NC_000913 | 3423895–3424229 | 3424394–3424237 | 9–500 | 22 [20] | [20] 22 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3581680 | 3582197 | 518 | 24 [18] | [20] 22 | [yhhZ] | [yhhZ] |
| * | * | ÷ | NC_000913 | 3769553 | 3770077 | 525 | 22 [20] | [17] 23 | [yibV]–[yibU] | [yibV], yibV, yibU, [yibU] |
| * | * | ÷ | NC_000913 | 3798635 | 3799652 | 1018 | 23 [21] | [19] 22 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 4268444 | 4268724 | 281 | 22 [21] | [21] 25 | tyrB/yjbS | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 224910 = | NA (NA) | 5 (0.060) | 4/498 | NT | NA | noncoding (1140/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 225157 = | NA (NA) | noncoding (1387/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 231791 | 72 (0.910) | 3 (0.040) | 3/506 | NT | 3.6% | coding (670/801 nt) | yafD | endo/exonuclease/phosphatase family protein |
| ? | NC_000913 | = 231901 | 91 (1.160) | coding (780/801 nt) | yafD | endo/exonuclease/phosphatase family protein | |||||
| * | ? | NC_000913 | = 243009 | 91 (1.140) | 5 (0.060) | 3/500 | NT | 5.1% | coding (295/2445 nt) | fadE | acyl coenzyme A dehydrogenase |
| ? | NC_000913 | = 243192 | 96 (1.240) | coding (112/2445 nt) | fadE | acyl coenzyme A dehydrogenase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 56 (0.700) | 43/514 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 379965 = | 52 (0.650) | 4 (0.050) | 4/504 | NT | 6.8% | intergenic (‑84/+104) | frmR/yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| ? | NC_000913 | 380853 = | 58 (0.740) | pseudogene (408/417 nt) | yaiX | pseudogene, interrupted by IS2A, hexapeptide transferase superfamily, putative transferase | |||||
| * | ? | NC_000913 | = 836651 | 84 (1.060) | 3 (0.040) | 3/494 | NT | 3.4% | coding (301/1086 nt) | ybiC | putative dehydrogenase |
| ? | NC_000913 | = 836897 | 89 (1.160) | coding (547/1086 nt) | ybiC | putative dehydrogenase | |||||
| * | ? | NC_000913 | = 969597 | 74 (0.930) | 4 (0.050) | 3/504 | NT | 4.7% | coding (209/1233 nt) | ycaQ | DUF1006 family protein with C‑terminal wHTH domain |
| ? | NC_000913 | = 969716 | 91 (1.170) | coding (328/1233 nt) | ycaQ | DUF1006 family protein with C‑terminal wHTH domain | |||||
| * | ? | NC_000913 | 1207790 = | 36 (0.450) | 41 (0.550) | 29/482 | NT | 57.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 26 (0.350) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 33 (0.410) | 52 (0.700) | 44/482 | NT | 64.6% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 26 (0.350) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 70 (0.880) | 51/514 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1731973 | 73 (0.920) | 4 (0.050) | 4/494 | NT | 5.5% | coding (2887/4617 nt) | lhr | putative ATP‑dependent helicase |
| ? | NC_000913 | = 1732058 | 66 (0.860) | coding (2972/4617 nt) | lhr | putative ATP‑dependent helicase | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 36 (0.450) | 28/514 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 49 (0.620) | 37/514 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2270127 = | 92 (1.160) | 8 (0.100) | 8/514 | NT | 8.0% | coding (151/567 nt) | mepS | murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein, weak murein LD‑carboxypeptidase |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2288917 = | NA (NA) | 3 (0.040) | 3/514 | NT | 5.4% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 2876676 = | 53 (0.670) | coding (98/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 7 (0.090) | 7/514 | NT | 11.9% | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| ? | NC_000913 | = 2876679 | 52 (0.650) | coding (101/1038 nt) | iap | aminopeptidase in alkaline phosphatase isozyme conversion | |||||
| * | ? | NC_000913 | = 2531963 | 62 (0.780) | 4 (0.050) | 3/494 | NT | 4.9% | coding (503/762 nt) | cysZ | sulfate transporter, sulfite inhibited |
| ? | NC_000913 | = 2532165 | 96 (1.260) | coding (705/762 nt) | cysZ | sulfate transporter, sulfite inhibited | |||||
| * | ? | NC_000913 | 2626064 = | 59 (0.740) | 3 (0.040) | 3/496 | NT | 4.0% | coding (952/1542 nt) | ppx | exopolyphosphatase |
| ? | NC_000913 | 2626614 = | 87 (1.130) | coding (1502/1542 nt) | ppx | exopolyphosphatase | |||||
| * | ? | NC_000913 | 2881788 = | 67 (0.840) | 4 (0.050) | 4/506 | NT | 7.4% | coding (353/1092 nt) | casC | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| ? | NC_000913 | 2882110 = | 34 (0.430) | coding (31/1092 nt) | casC | CRISP RNA (crRNA) containing Cascade antiviral complex protein | |||||
| * | ? | NC_000913 | = 3197494 | 81 (1.020) | 4 (0.050) | 3/500 | NT | 4.9% | coding (2146/2841 nt) | glnE | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| ? | NC_000913 | = 3197781 | 76 (0.980) | coding (1859/2841 nt) | glnE | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase | |||||
| * | ? | NC_000913 | = 3652918 | NA (NA) | 3 (0.040) | 3/506 | NT | 6.0% | coding (280/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913 | = 3655092 | 48 (0.600) | coding (411/531 nt) | dctR | Putative LuxR family repressor for dicarboxylate transport | |||||
| * | ? | NC_000913 | 3837737 = | 46 (0.580) | 3 (0.040) | 3/506 | NT | 4.1% | coding (786/1185 nt) | setC | putative arabinose efflux transporter |
| ? | NC_000913 | 3839188 = | 95 (1.210) | coding (805/819 nt) | nlpA | cytoplasmic membrane lipoprotein‑28 | |||||
| * | ? | NC_000913 | 3857725 = | 88 (1.110) | 4 (0.050) | 4/496 | NT | 4.6% | coding (679/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein |
| ? | NC_000913 | 3858257 = | 80 (1.040) | coding (147/1494 nt) | yidJ | sulfatase/phosphatase superfamily protein | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 9 (0.130) | 4/436 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4409626 = | 83 (1.040) | 3 (0.040) | 3/494 | NT | 4.0% | coding (351/732 nt) | rlmB | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | NC_000913 | 4409709 = | 66 (0.860) | coding (434/732 nt) | rlmB | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 4447213 | 108 (1.360) | 3 (0.040) | 3/494 | NT | 2.9% | coding (3101/3780 nt) | tamB | translocation and assembly module for autotransporter export, inner membrane subunit |
| ? | NC_000913 | = 4447555 | 95 (1.240) | coding (3443/3780 nt) | tamB | translocation and assembly module for autotransporter export, inner membrane subunit | |||||
| * | ? | NC_000913 | = 4552075 | 99 (1.240) | 4 (0.050) | 4/500 | NT | 4.2% | coding (439/1185 nt) | uxuA | mannonate hydrolase |
| ? | NC_000913 | = 4552347 | 86 (1.110) | coding (711/1185 nt) | uxuA | mannonate hydrolase | |||||