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 |
| RA | 66,691 | C→T | 5.7% | intergenic (‑141/+144) | araD ← / ← araA | L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase |
| RA | 94,212 | A→T | 3.7% | P349P (CCA→CCT) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 449,747 | A→G | 3.0% | S299P (TCC→CCC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 619,419 | G→A | 5.3% | L261F (CTC→TTC) | fepC ← | ferrienterobactin ABC transporter ATPase |
| RA | 659,936 | Δ1 bp | 3.1% | coding (281/966 nt) | lipA ← | lipoate synthase |
| RA | 832,070 | G→T | 3.4% | G400V (GGG→GTG) | rhlE → | ATP‑dependent RNA helicase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,466,276 | T→C | 9.1% | pseudogene (885/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,472,262 | G→A | 3.3% | pseudogene (1746/3497 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,547,552 | Δ1 bp | 5.2% | coding (152/3048 nt) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,724,800 | A→G | 6.0% | L278P (CTG→CCG) | ydhF ← | putative oxidoreductase |
| RA | 1,895,423 | G→T | 4.4% | G207C (GGT→TGT) | pabB → | aminodeoxychorismate synthase, subunit I |
| RA | 1,932,240 | G→A | 3.9% | L173L (CTG→TTG) | eda ← | KHG/KDPG aldolase, 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| JC | 1,987,795 | (TAG)2→1 | 4.2% | intergenic (‑37/+76) | yecJ ← / ← azuC | DUF2766 family protein/acid‑inducible small membrane‑associated protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,222,583 | T→C | 4.3% | L134P (CTG→CCG) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,346,536 | G→A | 3.3% | L558L (CTG→CTA) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,842,163 | C→T | 3.7% | R392R (CGC→CGT) | ascB → | cryptic 6‑phospho‑beta‑glucosidase |
| RA | 3,001,721 | Δ1 bp | 4.1% | coding (1379/2259 nt) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,194,706 | G→A | 4.7% | intergenic (+183/+15) | yqiK → / ← sibD | PHB family membrane protein, function unknown/sRNA antisense regulator of toxic IbsD protein |
| RA | 3,289,866 | A→T | 4.4% | Q352L (CAG→CTG) | yraJ → | putative outer membrane protein |
| RA | 3,344,212:1 | +C | 4.6% | coding (271/726 nt) | lptB → | lipopolysaccharide export ABC transporter ATPase |
| RA | 3,506,695 | C→T | 3.6% | G214R (GGG→AGG) | yhfT ← | inner membrane protein |
| RA | 3,682,529 | C→G | 4.9% | S306S (TCG→TCC) | dctA ← | C4‑dicarboxylic acid, orotate and citrate transporter |
| RA | 3,777,087 | C→T | 4.8% | intergenic (+61/‑311) | yibL → / → lldP | ribosome‑associated DUF2810 family protein/L‑lactate permease |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,862,012 | T→C | 4.9% | pseudogene (1591/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,929,583 | Δ1 bp | 4.1% | coding (20/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,584 | Δ1 bp | 4.0% | coding (19/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,585 | Δ1 bp | 4.0% | coding (18/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,586 | Δ1 bp | 4.0% | coding (17/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,587 | Δ1 bp | 3.8% | coding (16/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,588 | Δ1 bp | 3.9% | coding (15/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,589 | Δ1 bp | 3.8% | coding (14/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,590 | Δ1 bp | 3.8% | coding (13/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,929,591 | Δ1 bp | 3.8% | coding (12/1452 nt) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,939,335 | A→T | 4.4% | V426D (GTC→GAC) | hsrA ← | putative multidrug or homocysteine efflux system |
| RA | 3,951,247 | C→T | 3.1% | pseudogene (689/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive, acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,970,372 | Δ1 bp | 2.6% | coding (241/1131 nt) | wecB → | UDP‑N‑acetyl glucosamine‑2‑epimerase |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,186,085 | C→A | 100% | P246Q (CCG→CAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,189 | A→G | 36.9% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 35.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,334,956 | T→C | 3.6% | A212A (GCA→GCG) | eptA ← | lipid A phosphoethanolamine transferase |
| RA | 4,517,302 | C→T | 4.3% | V139V (GTG→GTA) | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport, periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,524,918 | A→G | 4.8% | F32L (TTC→CTC) | yjhH ← | putative lyase/synthase |
| RA | 4,569,139 | G→A | 4.9% | pseudogene (141/921 nt) | yjiP → | pseudogene, transposase_31 family protein |
| RA | 4,582,312 | C→T | 4.4% | L246L (CTG→CTA) | hsdM ← | DNA methyltransferase M |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 583093 | 584689 | 1597 | 30 [28] | [28] 37 | [tfaX]–[ompT] | [tfaX], appY, [ompT] |
| * | * | ÷ | NC_000913 | 720832 | 721152 | 321 | 31 [29] | [29] 31 | [ybfK]–[kdpE] | [ybfK], [kdpE] |
| * | * | ÷ | NC_000913 | 1211649 | 1212801 | 1153 | 30 [28] | [29] 30 | iraM–[ycgX] | iraM, [ycgX] |
| * | * | ÷ | NC_000913 | 1299473 | 1300758 | 1286 | 30 [27] | [28] 30 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1465080 | 1465326 | 247 | 30 [28] | [27] 30 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 1529963 | 1530438 | 476 | 31 [28] | [27] 30 | [ydcD] | [ydcD] |
| * | * | ÷ | NC_000913 | 2470044 | 2470613 | 570 | 30 [28] | [29] 30 | [gtrS] | [gtrS] |
| * | * | ÷ | NC_000913 | 2994994 | 2995649 | 656 | 31 [29] | [27] 30 | [ygeK]–[ygeN] | [ygeK], [ygeN] |
| * | * | ÷ | NC_000913 | 3423888–3424230 | 3424398–3424238 | 9–511 | 30 [29] | [29] 30 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3769495 | 3770238 | 744 | 30 [27] | [29] 30 | [yibV]–yibU | [yibV], yibV, yibU, yibU |
| * | * | ÷ | NC_000913 | 3798768 | 3799691 | 924 | 32 [26] | [28] 30 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 4233682 | 4235856 | 2175 | 31 [29] | [29] 30 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 74 (0.870) | 56/514 | NT | 98.7% | 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 | 1 (0.010) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 315229 = | 74 (0.870) | 4 (0.050) +TC |
4/510 | NT | 5.2% | intergenic (+1/‑62) | eaeH/insE1 | pseudogene, attaching and effacing protein homology,factor, Not classified/IS3 transposase A |
| ? | NC_000913 | = 2157512 | 74 (0.870) | coding (2250/3123 nt) | mdtB | multidrug efflux system, subunit B | |||||
| * | ? | NC_000913 | 1207790 = | 38 (0.450) | 47 (0.590) | 41/482 | NT | 55.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 39 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 35 (0.410) | 63 (0.790) | 43/482 | NT | 63.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 39 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 72 (0.850) | 50/514 | 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 | = 1299498 | 0 (0.000) | 24 (0.290) | 20/506 | 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 | 1411899 = | 83 (0.980) | 4 (0.050) | 4/462 | NT | 7.0% | coding (50/936 nt) | ttcA | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
| ? | NC_000913 | = 1434958 | 32 (0.420) | pseudogene (51/51 nt) | ttcC | pseudogene, prophage Rac integration site ttcA duplication,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1650843 = | 105 (1.240) | 5 (0.060) +CCCGACGATAACCATACGT |
3/476 | NT | 4.9% | intergenic (+1/‑2) | ydfE/insD1 | Qin prophage, pseudogene,Phage or Prophage Related/IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| ? | NC_000913 | 1650990 = | NA (NA) | pseudogene (146/693 nt) | insD1 | IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 80 (0.940) | 67/514 | NT | 100% | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/pseudogene, Qin prophage, phage integrase family,Phage or Prophage Related |
| ? | NC_000913 | = 1937140 | 0 (0.000) | coding (489/870 nt) | yebK | putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 1937136 = | 0 (0.000) | 47 (0.550) | 40/514 | NT | 100% | coding (485/870 nt) | yebK | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 2070271 | NA (NA) | intergenic (‑91/‑6) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 29 (0.350) | 26/498 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 37 (0.440) | 30/514 | 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) | 54 (0.640) | 43/514 | 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 | 3156577 = | 79 (0.930) | 4 (0.050) | 4/492 | NT | 5.4% | intergenic (+61/‑44) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| ? | NC_000913 | 3156601 = | 65 (0.800) | intergenic (+85/‑20) | yqhD/dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A | |||||
| * | ? | NC_000913 | 3652035 = | NA (NA) | 6 (0.070) | 6/514 | NT | 24.0% | intergenic (+5/+146) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913 | 4049890 = | 19 (0.220) | intergenic (+139/‑8) | polA/spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||
| * | ? | NC_000913 | = 3864716 | 102 (1.200) | 3 (0.040) | 3/502 | NT | 2.9% | coding (1557/1662 nt) | yidE | putative transporter |
| ? | NC_000913 | = 3864838 | 100 (1.200) | coding (1435/1662 nt) | yidE | putative transporter | |||||
| * | ? | NC_000913 | 4049912 = | 0 (0.000) | 53 (0.620) | 46/514 | NT | 100% | noncoding (15/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | 4498182 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology,IS, phage, Tn, Phage‑related functions and prophages, KpLE2 phage‑like element, P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | NC_000913 | = 4049918 | 0 (0.000) | 58 (0.690) | 47/510 | NT | 100% | noncoding (21/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499510 | NA (NA) | intergenic (+9/+84) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 3 (0.040) | 3/436 | 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 | |||||