mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 |
| RA | 7,286 | A→G | 5.3% | M225T (ATG→ACG) | yaaJ ← | putative transporter |
| RA | 88,862 | C→T | 3.4% | L279F (CTC→TTC) | cra → | transcriptional repressor‑activator for carbon metabolism |
| RA | 211,710 | A→G | 3.6% | M678V (ATG→GTG) | ldcC → | lysine decarboxylase 2, constitutive |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 356,312 | Δ1 bp | 2.9% | coding (142/1284 nt) | codA → | cytosine/isoguanine deaminase |
| RA | 444,803 | C→A | 3.1% | L41M (CTG→ATG) | yajQ → | phage Phi6 host factor, ATP/GTP binding protein |
| RA | 962,982 | G→C | 22.7% | V330L (GTT→CTT) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,020,956 | A→G | 32.8% | intergenic (‑37/‑182) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| RA | 1,039,661 | T→C | 4.0% | G122G (GGT→GGC) | cbdB → | cytochrome bd‑II oxidase, subunit II |
| RA | 1,148,138 | T→C | 4.0% | V173A (GTG→GCG) | plsX → | putative phosphate acyltransferase |
| RA | 1,222,581 | C→T | 3.9% | W18* (TGG→TGA) | ymgD ← | uncharacterized protein |
| RA | 1,287,037 | C→T | 13.0% | intergenic (+511/+29) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,595,007 | T→C | 4.4% | pseudogene (2981/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,677,913 | T→C | 61.4% | intergenic (‑10/‑514) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,722,065 | C→A | 3.8% | P268T (CCA→ACA) | ydhJ → | putative membrane fusion protein (MFP) of YdhJK efflux pump |
| RA | 1,851,115 | G→C | 3.7% | V86L (GTC→CTC) | ansA → | cytoplasmic L‑asparaginase 1 |
| 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 | 2,258,781 | C→T | 4.4% | V172I (GTC→ATC) | psuK ← | pseudouridine kinase |
| RA | 2,292,157 | C→T | 5.3% | V84V (GTG→GTA) | ccmH ← | heme lyase, CcmH subunit |
| RA | 2,665,308 | A→G | 4.3% | intergenic (+66/‑125) | yfhR → / → csiE | putative S9 family prolyl oligopeptidase/stationary phase inducible protein |
| RA | 2,912,201 | Δ1 bp | 7.9% | coding (1449/2235 nt) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,912,634 | C→T | 15.1% | R339H (CGC→CAC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,952,518 | C→T | 4.2% | A1162T (GCC→ACC) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 2,960,693 | Δ1 bp | 3.5% | coding (1734/3369 nt) | recC ← | exonuclease V (RecBCD complex), gamma chain |
| RA | 3,233,244 | T→G | 5.9% | F528V (TTC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,803,650 | C→T | 3.5% | V163I (GTC→ATC) | waaB ← | lipopolysaccharide 1,6‑galactosyltransferase, UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,005,738 | T→A | 3.2% | intergenic (+8/‑125) | pldA → / → recQ | outer membrane phospholipase A/ATP‑dependent DNA helicase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,295,833 | T→C | 9.6% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 8.9% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 45.6% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 43.8% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,346,817 | A→T | 5.3% | Y171N (TAC→AAC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,470,634 | A→G | 2.8% | F94S (TTC→TCC) | ridA ← | enamine/imine deaminase, reaction intermediate detoxification |
| RA | 4,491,427 | G→A | 4.1% | P367L (CCG→CTG) | idnT ← | L‑idonate and D‑gluconate transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2099630 | 2101384 | 1755 | 43 [40] | [31] 43 | gnd | gnd |
| * | * | ÷ | NC_000913 | 3423816–3424428 | 3424428 | 1–613 | 41 [35] | [40] 41 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 227039 | 56 (0.570) | 3 (0.030) | 3/510 | NT | 5.1% | noncoding (1281/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 227046 | 56 (0.580) | noncoding (1288/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 71 (0.720) | 52/522 | 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 | 1207790 = | 32 (0.330) | 41 (0.450) | 33/490 | NT | 57.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 31 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.320) | 56 (0.610) | 44/490 | NT | 65.1% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 31 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 79 (0.810) | 58/522 | 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 | = 1299498 | 0 (0.000) | 44 (0.460) | 37/514 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 67 (0.680) | 46/522 | 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) | 90 (0.920) | 57/522 | 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 | 2288917 = | NA (NA) | 19 (0.190) | 14/522 | NT | 25.3% | 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 | = 3578760 | 56 (0.570) | intergenic (‑35/+189) | gntR/yhhW | d‑gluconate inducible gluconate regulon transcriptional repressor/quercetinase activity in vitro | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 22 (0.230) | 21/520 | NT | 27.9% | intergenic (‑31/+2) | 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 | 3578756 = | 57 (0.580) | intergenic (‑31/+193) | gntR/yhhW | d‑gluconate inducible gluconate regulon transcriptional repressor/quercetinase activity in vitro | |||||
| * | ? | NC_000913 | = 3498079 | 91 (0.930) | 5 (0.050) | 5/504 | NT | 5.3% | coding (254/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| ? | NC_000913 | = 3498084 | 92 (0.970) | coding (259/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 12 (0.140) | 5/444 | 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 | 4464734 = | 89 (0.910) | 3 (0.030) | 3/486 | NT | 3.5% | intergenic (‑24/+26) | treC/treB | trehalose‑6‑P hydrolase/trehalose‑specific PTS enzyme: IIB and IIC component |
| ? | NC_000913 | 4464752 = | 85 (0.930) | intergenic (‑42/+8) | treC/treB | trehalose‑6‑P hydrolase/trehalose‑specific PTS enzyme: IIB and IIC component | |||||