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 | 199,346 | A→G | 3.2% | V473V (GTA→GTG) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| RA | 215,151 | C→T | 3.8% | P107S (CCC→TCC) | arfB → | alternative stalled‑ribosome rescue factor B, peptidyl‑tRNA hydrolase, ribosome‑attached |
| RA | 248,032 | G→A | 3.7% | W132* (TGG→TGA) | rayT → | RAYT REP element‑mobilizing transposase, TnpA(REP) |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 272,498 | T→C | 3.4% | intergenic (+309/‑82) | insN → / → eyeA | pseudogene, IS911 transposase A,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/novel sRNA, function unknown, CP4‑6 propahge |
| JC | 700,783 | Δ9 bp | 6.9% | coding (804‑812/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 701,938 | T→C | 3.4% | T272A (ACT→GCT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 702,331 | Δ1 bp | 4.9% | coding (421/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 762,772 | T→G | 2.7% | intergenic (+33/‑242) | sucB → / → sucC | dihydrolipoyltranssuccinase/succinyl‑CoA synthetase, beta subunit |
| RA | 880,827 | C→T | 3.7% | A34V (GCG→GTG) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase, penicillin‑binding protein 6a |
| RA | 1,158,171 | Δ1 bp | 3.9% | coding (303/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,158,383 | G→A | 4.6% | W172* (TGG→TAG) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC | 1,159,286:1 | +GTA | 16.8% | coding (1418/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,434,765 | T→C | 3.6% | intergenic (‑541/+193) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication,Phage or Prophage Related |
| RA | 1,466,435 | A→G | 4.3% | pseudogene (1044/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,571,844 | C→T | 4.1% | D68N (GAC→AAC) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| JC | 1,606,911 | Δ3 bp | 3.2% | coding (812‑814/876 nt) | lsrF → | putative autoinducer‑2 (AI‑2) aldolase |
| RA | 1,708,844 | C→G | 8.4% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,930 | C→A | 9.9% | P671Q (CCG→CAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,994 | A→C | 7.0% | A692A (GCA→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,911,301 | C→A | 3.9% | F342L (TTC→TTA) | yebQ → | putative transporter |
| 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 | 2,304,520 | G→T | 8.1% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,521 | G→C | 8.9% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,535 | A→G | 8.7% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,538 | C→T | 10.9% | intergenic (+147/+568) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,547 | C→T | 8.5% | intergenic (+156/+559) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,314,714 | C→A | 8.3% | A410E (GCG→GAG) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,315,751 | G→A | 2.9% | G756S (GGC→AGC) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| JC | 2,521,128 | Δ122 bp | 5.2% | valY | valY | |
| RA | 2,736,370 | T→A | 2.9% | I76N (ATC→AAC) | bamD → | BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,873,546 | Δ1 bp | 3.1% | coding (445/606 nt) | cysC ← | adenosine 5'‑phosphosulfate kinase |
| RA | 2,911,224 | Δ1 bp | 3.0% | coding (114/249 nt) | mazE ← | antitoxin of the ChpA‑ChpR toxin‑antitoxin system |
| RA | 2,951,194 | C→A | 3.5% | L422L (CTG→CTT) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 3,054,069 | A→G | 5.2% | L257P (CTG→CCG) | pepP ← | proline aminopeptidase P II |
| RA | 3,059,204 | A→G | 3.2% | G40G (GGT→GGC) | rpiA ← | ribose 5‑phosphate isomerase, constitutive |
| RA | 3,074,077 | G→C | 3.0% | A204G (GCC→GGC) | yggC ← | putative PanK family P‑loop kinase |
| RA | 3,103,813 | A→G | 4.1% | E268G (GAA→GGA) | mutY → | adenine DNA glycosylase |
| RA | 3,509,246 | A→T | 3.6% | L189* (TTA→TAA) | yhfW ← | phosphopentomutase‑related metalloenzyme superfamily protein |
| RA | 3,510,330 | T→A | 2.8% | I215I (ATA→ATT) | yhfX ← | putative pyridoxal 5'‑phosphate binding protein |
| RA | 3,688,258 | A→G | 10.0% | A305A (GCT→GCC) | bcsC ← | cellulose synthase subunit |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,875,532 | T→G | 9.3% | H32Q (CAT→CAG) | yidX → | putative lipoprotein |
| MC JC | 3,909,311 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,952,577 | Δ1 bp | 2.9% | coding (95/930 nt) | ilvE → | branched‑chain amino acid aminotransferase |
| JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,085,630 | G→T | 3.0% | L64L (CTC→CTA) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,097,902:1 | +C | 3.7% | coding (168/837 nt) | rhaS → | transcriptional activator of rhaBAD and rhaT |
| RA | 4,171,647 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,189 | A→G | 32.8% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 38.0% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 21.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,285 | C→T | 11.2% | intergenic (+492/+152) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,379,106 | G→A | 2.5% | H88Y (CAC→TAC) | frdD ← | fumarate reductase (anaerobic), membrane anchor subunit |
| RA | 4,409,597 | A→T | 3.4% | N108Y (AAC→TAC) | rlmB → | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 4,472,237 | T→G | 18.0% | T54P (ACC→CCC) | pyrB ← | aspartate carbamoyltransferase, catalytic subunit |
| RA | 4,490,242 | C→A | 2.6% | R300L (CGG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,562,673 | G→T | 3.5% | P2T (CCT→ACT) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| JC | 4,606,167 | Δ121 bp | 5.1% | [leuP] | [leuP] | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1465060 | 1465377 | 318 | 51 [50] | [50] 52 | [paaY]–ynbG | [paaY], ynbG |
| * | * | ÷ | NC_000913 | 3423869–3424447 | 3424447 | 1–579 | 51 [49] | [50] 51 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4110676 | 4111543 | 868 | 51 [47] | [50] 51 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 91 (0.750) | 62/520 | 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 | 852936 = | 140 (1.160) | 4 (0.030) | 3/504 | NT | 2.8% | coding (62/129 nt) | mntS | Mn(2)‑response protein, MntR‑repressed |
| ? | NC_000913 | 854010 = | 139 (1.180) | coding (364/1119 nt) | ybiR | putative transporter | |||||
| * | ? | NC_000913 | 1159285 = | 105 (0.870) | 9 (0.070) | 9/516 | NT | 8.0% | coding (1417/1434 nt) | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| ? | NC_000913 | = 1469238 | NA (NA) | intergenic (‑89/‑3) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog, interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913 | = 1159291 | 98 (0.810) | 5 (0.040) | 5/520 | NT | 4.9% | coding (1423/1434 nt) | ptsG | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| ? | NC_000913 | = 1651548 | NA (NA) | 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 | 1207790 = | 50 (0.410) | 42 (0.370) | 37/488 | NT | 47.2% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 47 (0.410) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.400) | 51 (0.450) | 43/488 | NT | 52.6% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 47 (0.410) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 119 (0.980) | 73/520 | 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) | 57 (0.480) | 44/512 | 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) | 65 (0.540) | 49/520 | 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) | 104 (0.860) | 60/520 | 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 | = 2713827 | 116 (0.960) | 4 (0.030) | 4/498 | NT | 3.6% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase |
| ? | NC_000913 | = 2713906 | 101 (0.870) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase | |||||
| * | ? | NC_000913 | 3989868 = | 116 (0.960) | 4 (0.030) | 3/504 | NT | 3.6% | coding (898/942 nt) | hemC | hydroxymethylbilane synthase |
| ? | NC_000913 | 3989976 = | 104 (0.890) | coding (790/942 nt) | hemC | hydroxymethylbilane synthase | |||||