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 | 124,241 | C→T | 100% | Q409* (CAG→TAG) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 151,519 | A→C | 9.3% | I27M (ATT→ATG) | yadK ← | putative fimbrial protein YadK |
| RA | 151,522 | G→T | 8.8% | A26A (GCC→GCA) | yadK ← | putative fimbrial protein YadK |
| RA | 231,007 | C→A | 8.2% | intergenic (‑126/‑115) | yafC ← / → yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| RA | 231,008 | T→G | 8.4% | intergenic (‑127/‑114) | yafC ← / → yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,882 | T→G | 10.7% | I163S (ATC→AGC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 449,135 | C→A | 100% | V503L (GTA→TTA) | cyoB ← | cytochrome bo3 ubiquinol oxidase subunit 1 |
| RA | 454,891 | G→T | 100% | intergenic (+102/‑242) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 461,010 | C→A | 100% | T708N (ACT→AAT) | lon → | Lon protease |
| RA | 481,225 | T→G | 7.7% | intergenic (‑517/+29) | tomB ← / ← acrB | protein that modulates Hha toxicity/multidrug efflux pump RND permease AcrB |
| RA | 595,519 | T→A | 7.9% | intergenic (‑76/‑81) | cusR ← / → cusC | DNA‑binding transcriptional activator CusR/copper/silver export system outer membrane channel |
| RA | 696,470 | C→T | 100% | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 754,446 | A→G | 100% | L8P (CTC→CCC) | gltA ← | citrate synthase |
| RA | 760,485 | G→A | 100% | G594S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,597,272 | T→A | 9.2% | pseudogene (815/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,801,361 | C→A | 100% | V404F (GTC→TTC) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,837,091 | T→C | 8.8% | V340A (GTT→GCT) | ynjB → | putative ABC transporter periplasmic binding protein YnjB |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 1,987,442 | Δ1 bp | 9.8% | intergenic (+14/+65) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 1,987,450:1 | +A | 8.0% | intergenic (+22/+57) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,368,101 | T→C | 100% | A21A (GCT→GCC) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,392,235 | G→T | 100% | Y269* (TAC→TAA) | nuoM ← | NADH:quinone oxidoreductase subunit M |
| RA | 2,653,104 | G→C | 10.4% | W204S (TGG→TCG) ‡ | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,653,105 | G→C | 8.7% | W204C (TGG→TGC) ‡ | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,661,821 | C→G | 100% | C104S (TGC→TCC) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,800,515 | C→A | 7.8% | intergenic (+40/‑208) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 2,800,517 | T→A | 7.3% | intergenic (+42/‑206) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 2,800,519 | T→G | 6.7% | intergenic (+44/‑204) | ygaM → / → nrdH | DUF883 domain‑containing protein YgaM/glutaredoxin‑like protein |
| RA | 3,041,634 | A→C | 100% | T108P (ACC→CCC) | ygfZ → | folate‑binding protein |
| RA | 3,334,704 | G→C | 10.4% | intergenic (+23/‑205) | ispB → / → sfsB | all‑trans‑octaprenyl‑diphosphate synthase/putative transcriptional regulator SfsB |
| RA | 3,512,306 | G→C | 8.8% | I13M (ATC→ATG) | yhfZ ← | putative DNA‑binding transcriptional regulator YhfZ |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph] | [rph] | |
| RA | 3,938,255 | T→A | 7.2% | L10Q (CTG→CAG) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | Ni(2(+))/Co(2(+))/Mg(2(+)) transporter |
| RA | 4,033,565 | G→A | 100% | G141R (GGG→AGG) | trkH → | K(+) transporter TrkH |
| RA | 4,056,531 | A→G | 7.1% | intergenic (‑192/+94) | glnL ← / ← glnA | sensory histidine kinase NtrB/glutamine synthetase |
| RA | 4,056,539 | T→A | 6.4% | intergenic (‑200/+86) | glnL ← / ← glnA | sensory histidine kinase NtrB/glutamine synthetase |
| RA | 4,056,540 | T→A | 6.4% | intergenic (‑201/+85) | glnL ← / ← glnA | sensory histidine kinase NtrB/glutamine synthetase |
| RA | 4,159,079 | G→T | 100% | G197V (GGT→GTT) | oxyR → | DNA‑binding transcriptional dual regulator OxyR |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase subunit beta |
| RA | 4,196,203 | C→T | 100% | intergenic (‑104/+129) | thiC ← / ← rsd | phosphomethylpyrimidine synthase/regulator of sigma D |
| RA | 4,296,060 | C→T | 26.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,551,422 | T→A | 9.4% | intergenic (‑126/‑214) | gntP ← / → uxuA | fructuronate transporter/D‑mannonate dehydratase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 315646 | NA (NA) | 9 (0.230) | 8/254 | NT | NA | noncoding (418/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315665 | NA (NA) | noncoding (437/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315843 = | NA (NA) | 3 (0.070) | 3/258 | NT | NA | noncoding (615/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315886 = | NA (NA) | noncoding (658/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 392478 = | NA (NA) | 7 (0.170) | 6/260 | NT | NA | noncoding (489/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 392552 = | NA (NA) | noncoding (415/1258 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 566777 = | NA (NA) | 1854 (45.540) | 248/262 | NT | 97.6% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 572471 | 46 (1.120) | coding (6/456 nt) | ybcN | DLP12 prophage; DNA base‑flipping protein | |||||
| * | ? | NC_000913 | 882488 = | 38 (0.930) | 3 (0.080) | 3/254 | NT | 7.4% | coding (247/759 nt) | deoR | DNA‑binding transcriptional repressor DeoR |
| ? | NC_000913 | 882517 = | 38 (0.960) | coding (218/759 nt) | deoR | DNA‑binding transcriptional repressor DeoR | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.150) | 26 (0.720) | 26/232 | NT | 83.5% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 5 (0.140) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.150) | 16 (0.440) | 14/232 | NT | 75.7% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 5 (0.140) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1463437 | 56 (1.360) | 6 (0.150) | 5/262 | NT | 9.7% | coding (1313/1314 nt) | paaK | phenylacetate‑CoA ligase |
| ? | NC_000913 | = 1463490 | 56 (1.380) | intergenic (+52/‑49) | paaK/paaX | phenylacetate‑CoA ligase/DNA‑binding transcriptional repressor PaaX | |||||
| * | ? | NC_000913 | 2422747 = | 45 (1.100) | 3 (0.080) | 3/250 | NT | 6.8% | coding (793/891 nt) | rpnB | recombination‑promoting nuclease RpnB |
| ? | NC_000913 | 2422773 = | 39 (1.000) | coding (767/891 nt) | rpnB | recombination‑promoting nuclease RpnB | |||||
| * | ? | NC_000913 | = 2700077 | 41 (1.000) | 3 (0.080) | 3/240 | NT | 7.1% | intergenic (+154/+40) | yfhL/shoB | putative 4Fe‑4S cluster‑containing protein YfhL/toxic peptide ShoB |
| ? | NC_000913 | = 2700087 | 41 (1.100) | intergenic (+164/+30) | yfhL/shoB | putative 4Fe‑4S cluster‑containing protein YfhL/toxic peptide ShoB | |||||
| * | ? | NC_000913 | 3603658 = | 48 (1.170) | 3 (0.080) | 3/250 | NT | 6.4% | coding (586/1494 nt) | ftsY | signal recognition particle receptor |
| ? | NC_000913 | 3603682 = | 43 (1.110) | coding (562/1494 nt) | ftsY | signal recognition particle receptor | |||||
| * | ? | NC_000913 | = 3620220 | NA (NA) | 3 (0.080) | 3/252 | NT | 100% | coding (1029/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620255 | 0 (0.000) | coding (1064/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 4323298 = | NA (NA) | 3 (0.080) | 3/250 | NT | NA | noncoding (1/36 nt) | other | REP324b |
| ? | NC_000913 | 4323328 = | NA (NA) | noncoding (31/36 nt) | other | REP324b | |||||
| * | ? | NC_000913 | = 4338123 | 35 (0.850) | 3 (0.080) | 3/252 | NT | 7.9% | intergenic (‑194/+131) | adiY/adiA | DNA‑binding transcriptional activator AdiY/arginine decarboxylase, degradative |
| ? | NC_000913 | = 4338130 | 37 (0.950) | intergenic (‑201/+124) | adiY/adiA | DNA‑binding transcriptional activator AdiY/arginine decarboxylase, degradative | |||||
| * | ? | NC_000913 | = 4383657 | 51 (1.240) | 3 (0.080) | 3/246 | NT | 5.7% | intergenic (+37/‑182) | epmA/yjeM | EF‑P‑lysine lysyltransferase/putative transporter YjeM |
| ? | NC_000913 | = 4383664 | 51 (1.330) | intergenic (+44/‑175) | epmA/yjeM | EF‑P‑lysine lysyltransferase/putative transporter YjeM | |||||