mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 119,295 | A→T | 5.7% | T5T (ACA→ACT) | ampE → | ampicillin resistance inner membrane protein; putative signaling protein in beta‑lactamase regulation |
| RA | 219,763 | T→C | 5.6% | N78S (AAT→AGT) | rcsF ← | putative outer membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 285,882 | T→G | 5.2% | I163S (ATC→AGC) | yagG → | CP4‑6 prophage; putative sugar transporter |
| RA | 285,887 | C→A | 6.0% | L165M (CTG→ATG) | yagG → | CP4‑6 prophage; putative sugar transporter |
| RA | 326,821 | C→T | 5.2% | G143S (GGC→AGC) | betA ← | choline dehydrogenase, a flavoprotein |
| RA | 384,328 | C→A | 5.3% | D97Y (GAT→TAT) | yaiS ← | putative PIG‑L family deacetylase |
| JC JC | 564,107 | IS2 (+) +5 bp | 100% | coding (370‑374/633 nt) | sfmZ ← | response regulator family protein |
| RA | 741,486 | G→A | 5.5% | A357A (GCC→GCT) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 756,303 | C→A | 92.4% | R133S (CGC→AGC) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 786,623 | T→C | 5.1% | W331R (TGG→CGG) | aroG → | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, phenylalanine repressible |
| RA | 875,401 | G→T | 6.9% | A23S (GCC→TCC) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 897,081 | C→T | 5.8% | H316H (CAC→CAT) | potH → | putrescine ABC transporter permease |
| RA | 942,026 | C→G | 5.5% | A356A (GCC→GCG) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 945,863 | T→C | 5.8% | intergenic (‑306/‑8) | ycaC ← / → ycaD | putative isochorismatase family hydrolase/putative MFS transporter, inner membrane protein |
| RA | 987,560 | G→C | 5.1% | intergenic (‑578/+25) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 987,561 | G→C | 5.1% | intergenic (‑579/+24) | ompF ← / ← asnS | outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase |
| RA | 1,048,285 | A→C | 8.4% | V136G (GTC→GGC) | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,194,176 | A→G | 6.0% | L38P (CTG→CCG) | nudJ ← | bifunctional thiamine pyrimidine pyrophosphate hydrolase and thiamine pyrophosphate hydrolase |
| RA | 1,221,641 | T→A | 7.4% | pseudogene (2041/2574 nt) | ycgH → | pseudogene; putative ATP‑binding component of a transport system |
| RA | 1,224,829 | A→G | 5.5% | L178P (CTG→CCG) | minD ← | inhibitor of FtsZ ring polymerization; chromosome‑membrane tethering protein; membrane ATPase of the MinCDEE system |
| RA | 1,286,766 | T→G | 9.0% | intergenic (+240/+300) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,767 | G→C | 8.8% | intergenic (+241/+299) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,286,768 | C→A | 9.4% | intergenic (+242/+298) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,288,332 | A→G | 5.1% | L98P (CTT→CCT) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,314,261 | C→T | 6.5% | P81L (CCG→CTG) | ompW → | outer membrane protein W |
| RA | 1,428,271 | A→C | 8.4% | S152S (TCT→TCG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 1,452,259 | C→T | 5.9% | G462R (GGG→AGG) | paaZ ← | oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,452,273 | G→A | 5.2% | A457V (GCA→GTA) | paaZ ← | oxepin‑CoA hydrolase and 3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,466,891 | C→T | 5.4% | pseudogene (1500/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,514,378 | C→T | 6.5% | S183F (TCC→TTC) | ydcU → | putative ABC transporter permease |
| RA | 1,533,930 | T→G | 6.2% | intergenic (‑79/‑94) | yddH ← / → nhoA | flavin reductase like‑protein/N‑hydroxyarylamine O‑acetyltransferase |
| RA | 1,552,085 | G→T | 7.3% | intergenic (+94/+313) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,606,548 | A→T | 5.3% | H150L (CAT→CTT) | lsrF → | putative autoinducer‑2 (AI‑2) aldolase |
| RA | 1,612,353 | G→A | 5.5% | T300M (ACG→ATG) | glsB ← | glutaminase 2 |
| RA | 1,612,716 | C→T | 5.1% | G179D (GGC→GAC) | glsB ← | glutaminase 2 |
| RA | 1,622,975 | C→G | 5.6% | V292V (GTG→GTC) | dgcZ ← | diguanylate cyclase, zinc‑sensing |
| RA | 1,671,548 | A→G | 5.2% | Q58R (CAG→CGG) | asr → | acid shock‑inducible periplasmic protein |
| RA | 1,715,919 | T→G | 5.6% | intergenic (‑30/+29) | pdxY ← / ← tyrS | pyridoxamine kinase/tyrosyl‑tRNA synthetase |
| RA | 1,715,920 | T→A | 5.2% | intergenic (‑31/+28) | pdxY ← / ← tyrS | pyridoxamine kinase/tyrosyl‑tRNA synthetase |
| RA | 1,729,944 | T→C | 6.7% | L286L (CTT→CTC) | lhr → | putative ATP‑dependent helicase |
| RA | 1,733,378 | A→G | 10.2% | N1431S (AAT→AGT) | lhr → | putative ATP‑dependent helicase |
| RA | 1,750,351 | A→G | 5.2% | N221N (AAT→AAC) | ydhX ← | putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex |
| RA | 1,855,344 | T→A | 7.9% | N210Y (AAT→TAT) | ydjG ← | methylglyoxal reductase, NADH‑dependent |
| RA | 1,862,688 | A→G | 5.0% | intergenic (‑259/‑83) | msrB ← / → gapA | methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,900,088 | Δ1 bp | 5.2% | coding (1498/1557 nt) | yoaE ← | putative membrane protein/conserved protein |
| RA | 1,922,524 | A→T | 5.5% | V149D (GTT→GAT) | pphA ← | serine/threonine‑specific protein phosphatase 1 |
| RA | 1,929,318 | T→C | 5.1% | Q130Q (CAA→CAG) | yebE ← | DUF533 family inner membrane protein |
| RA | 1,970,186 | G→A | 7.1% | R267C (CGT→TGT) | tap ← | methyl‑accepting protein IV |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,074,691 | C→G | 5.7% | intergenic (+33/‑88) | flu → / → yeeR | CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter/CP4‑44 prophage; putative membrane protein |
| RA | 2,085,969 | C→G | 5.6% | G365A (GGT→GCT) | plaP ← | putrescine importer, low affinity |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,311,616 | C→T | 5.1% | intergenic (‑82/+30) | apbE ← / ← ompC | putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C |
| RA | 2,311,619 | A→G | 5.3% | intergenic (‑85/+27) | apbE ← / ← ompC | putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C |
| RA | 2,357,836 | G→A | 5.1% | pseudogene (33/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,411,551 | G→A | 5.0% | A180V (GCG→GTG) | yfbT ← | sugar phosphatas |
| RA | 2,443,811 | T→C | 6.0% | intergenic (+41/+80) | mnmC → / ← yfcL | fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme/uncharacterized protein |
| RA | 2,506,444 | C→G | 5.6% | A63A (GCG→GCC) | ypdF ← | Xaa‑Pro aminopeptidase |
| RA | 2,516,520 | C→T | 7.4% | G438D (GGT→GAT) | yfeA ← | putative diguanylate cyclase |
| RA | 2,549,601 | T→G | 6.1% | intergenic (+195/+45) | yfeW → / ← yfeX | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic |
| RA | 2,552,185 | A→T | 5.2% | intergenic (‑47/‑167) | ypeA ← / → amiA | GNAT family putative N‑acetyltransferase/N‑acetylmuramoyl‑l‑alanine amidase I |
| RA | 2,560,985 | C→A | 21.2% | intergenic (+87/‑383) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,609,522 | C→T | 5.1% | Q346* (CAA→TAA) | hyfG → | hydrogenase 4, subunit |
| RA | 2,646,836 | C→T | 5.9% | A164T (GCT→ACT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| RA | 2,856,427 | C→A | 5.5% | intergenic (+11/+26) | fhlA → / ← ygbA | formate hydrogenlyase transcriptional activator/uncharacterized protein |
| RA | 2,918,497 | G→A | 5.1% | Q297* (CAA→TAA) | gudD ← | D‑glucarate dehydratase 1 |
| RA | 3,224,192 | A→G | 5.4% | G520G (GGA→GGG) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,270,069 | C→T | 6.8% | intergenic (+467/+147) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,569,442 | C→T | 5.6% | E626E (GAG→GAA) | glgX ← | glycogen debranching enzyme |
| RA | 3,959,515 | T→A | 10.1% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,182,929 | A→T | 100% | E562V (GAA→GTA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 27.8% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,323,257 | Δ1 bp | 5.4% | intergenic (‑27/+79) | phnE ← / ← phnD | defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily/phosphonate ABC transporter periplasmic binding protein |
| RA | 4,606,239 | A→G | 15.7% | noncoding (48/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 761497 | 762758 | 1262 | 27 [19] | [25] 26 | [sucA]–sucB | [sucA],sucB |
| * | * | ÷ | NC_000913 | 3423765–3424234 | 3424550–3424238 | 5–786 | 28 [24] | [24] 26 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381449 = | NA (NA) | 4 (0.050) | 3/242 | NT | NA | noncoding (190/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 381470 = | NA (NA) | noncoding (211/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.170) | 44 (0.560) | 38/214 | NT | 66.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 31 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.160) | 39 (0.500) | 29/214 | NT | 64.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 31 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1208513 = | 55 (0.610) | 4 (0.050) | 4/234 | NT | 6.9% | coding (382/414 nt) | tfaP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1208541 = | 56 (0.660) | coding (410/414 nt) coding (579/603 nt) |
tfaP tfaE |
e14 prophage; uncharacterized protein e14 prophage; putative tail fiber assembly protein |
|||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 105 (1.210) | 70/238 | 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 | 1396531 = | NA (NA) | 3 (0.040) | 3/234 | NT | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1972664 = | 72 (0.800) | 4 (0.050) | 4/238 | NT | 5.2% | coding (28/1662 nt) | tar | methyl‑accepting chemotaxis protein II |
| ? | NC_000913 | 1972676 = | 76 (0.880) | coding (16/1662 nt) | tar | methyl‑accepting chemotaxis protein II | |||||
| * | ? | NC_000913 | 4357635 = | 112 (1.250) | 6 (0.070) | 3/234 | NT | 5.5% | coding (983/2148 nt) | cadA | lysine decarboxylase, acid‑inducible |
| ? | NC_000913 | 4357654 = | 101 (1.180) | coding (964/2148 nt) | cadA | lysine decarboxylase, acid‑inducible | |||||