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 | 197,248 | G→A | 6.2% | A235T (GCA→ACA) | rseP → | inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease |
RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
RA | 305,971 | C→T | 5.2% | A283T (GCC→ACC) | ecpD ← | polymerized tip adhesin of ECP fibers |
RA | 331,406 | C→A | 7.5% | T648T (ACC→ACA) | betT → | choline transporter of high affinity |
RA | 531,546 | C→A | 5.8% | E226* (GAA→TAA) | allS ← | allD operon transcriptional activator |
RA | 566,173 | C→G | 14.0% | pseudogene (204/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
RA | 566,205 | T→C | 12.1% | pseudogene (172/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
RA | 566,245 | G→A | 8.9% | pseudogene (132/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
RA | 574,295 | G→T | 6.7% | D114Y (GAT→TAT) | quuD → | DLP12 prophage; putative antitermination protein |
RA | 581,133 | A→G | 8.8% | K100K (AAA→AAG) | nohD → | DLP12 prophage; DNA packaging protein |
RA | 581,185 | C→T | 10.9% | L118L (CTG→TTG) | nohD → | DLP12 prophage; DNA packaging protein |
RA | 581,227 | A→C | 22.4% | I132L (ATC→CTC) | nohD → | DLP12 prophage; DNA packaging protein |
RA | 737,043 | T→C | 5.6% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
RA | 737,928 | C→G | 6.4% | pseudogene (1104/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
RA | 805,325 | T→C | 5.7% | V608A (GTG→GCG) | ybhJ → | aconitase family protein |
RA | 915,213 | A→T | 16.7% | intergenic (‑356/+139) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
RA | 915,226 | T→G | 11.8% | intergenic (‑369/+126) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
RA | 1,049,827 | T→G | 5.3% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
RA | 1,086,485 | G→T | 6.2% | P12Q (CCA→CAA) | pgaD ← | biofilm PGA synthase PgaCD, regulatory subunit; c‑di‑GMP‑stimulated activity and dimerization |
RA | 1,092,203 | C→T | 5.1% | A29A (GCG→GCA) | pgaA ← | biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein |
RA | 1,113,077 | C→A | 5.6% | R739S (CGT→AGT) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
RA | 1,120,913 | C→A | 6.3% | G15W (GGG→TGG) | bssS ← | biofilm regulator |
RA | 1,269,897 | T→G | 8.8% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
RA | 1,386,010 | C→A | 6.1% | S167* (TCG→TAG) | ycjF → | UPF0283 family inner membrane protein |
RA | 1,402,454 | G→T | 5.5% | Q268K (CAG→AAG) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
RA | 1,405,953 | C→T | 10.2% | intergenic (‑202/‑26) | mcaS ← / → smrA | motility and biofilm regulator sRNA/DNA endonuclease |
RA | 1,411,384 | C→T | 10.5% | A189T (GCC→ACC) | ttcA ← | tRNA s(2)C32 thioltransferase, iron sulfur cluster protein |
RA | 1,451,132 | G→T | 7.5% | P73H (CCT→CAT) | tynA ← | tyramine oxidase, copper‑requiring |
RA | 1,476,962 | T→C | 6.6% | W607R (TGG→CGG) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
RA | 1,498,458 | T→C | 5.1% | F535L (TTC→CTC) | opgD → | OPG biosynthetic periplasmic protein |
RA | 1,517,534 | C→A | 6.0% | P49Q (CCG→CAG) | ydcX → | DUF2566 family protein |
RA | 1,571,296 | C→A | 6.7% | L250L (CTG→CTT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
RA | 1,610,940 | G→T | 7.9% | T305T (ACC→ACA) | yneF ← | putative membrane‑bound diguanylate cyclase |
RA | 1,635,293 | G→A | 7.5% | T185T (ACC→ACT) | stfQ ← | Qin prophage; putative side tail fibre assembly protein |
RA | 1,635,296 | T→G | 7.5% | G184G (GGA→GGC) | stfQ ← | Qin prophage; putative side tail fibre assembly protein |
RA | 1,635,322 | C→T | 5.6% | E176K (GAA→AAA) | stfQ ← | Qin prophage; putative side tail fibre assembly protein |
RA | 1,689,399 | C→T | 6.4% | A275V (GCG→GTG) | manA → | mannose‑6‑phosphate isomerase |
RA | 1,689,815 | G→T | 5.5% | intergenic (+64/‑37) | manA → / → ydgA | mannose‑6‑phosphate isomerase/DUF945 family protein |
RA | 1,782,761 | C→A | 7.2% | I27I (ATC→ATA) | ydiT → | putative 3Fe‑4S ferredoxin‑type protein |
RA | 1,919,279 | A→G | 11.6% | V590V (GTA→GTG) | yebT → | MCE domain protein |
RA | 1,941,612 | G→T | 5.3% | V8V (GTC→GTA) | mepM ← | murein DD‑endopeptidase, space‑maker hydrolase, septation protein |
RA | 1,975,135 | C→A | 5.7% | E64* (GAA→TAA) | cheA ← | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
RA | 2,013,898 | G→T | 5.5% | G224W (GGG→TGG) | fliF → | flagellar basal‑body MS‑ring and collar protein |
RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
RA | 2,046,785 | G→T | 5.7% | V616V (GTG→GTT) | yeeJ → | putative adhesin |
RA | 2,132,403 | G→T | 6.3% | I51I (ATC→ATA) | wcaB ← | putative acyl transferase |
RA | 2,147,021 | T→C | 94.6% | M174V (ATG→GTG) | alkA ← | 3‑methyl‑adenine DNA glycosylase II |
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 | 2,257,293 | C→G | 5.0% | A15P (GCA→CCA) | psuT ← | putative nucleoside transporter |
RA | 2,259,286 | T→C | 5.1% | K4R (AAG→AGG) | psuK ← | pseudouridine kinase |
RA | 2,297,107:1 | +C | 100% | coding (538/624 nt) | ccmA ← | heme export ABC transporter ATPase |
RA | 2,312,239 | G→T | 6.5% | Q171K (CAG→AAG) | ompC ← | outer membrane porin protein C |
JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
RA | 2,753,308 | T→C | 6.9% | V505A (GTC→GCC) | recN → | recombination and repair protein |
RA | 2,818,324 | G→A | 6.1% | intergenic (‑50/+149) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
RA | 2,818,331 | G→T | 5.9% | intergenic (‑57/+142) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
RA | 2,821,424 | G→C | 88.3% | G196G (GGC→GGG) | alaS ← | alanyl‑tRNA synthetase |
RA | 2,826,080 | G→T | 5.0% | M83I (ATG→ATT) | srlA → | glucitol/sorbitol‑specific enzyme IIC component of PTS |
RA | 2,859,142 | G→A | 90.1% | A684T (GCC→ACC) | mutS → | methyl‑directed mismatch repair protein |
RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
RA | 2,984,895 | G→T | 5.1% | P233H (CCT→CAT) | yqeF ← | short chain acyltransferase |
RA | 3,068,506 | G→T | 6.7% | A101A (GCC→GCA) | argO ← | arginine transporter |
RA | 3,116,386 | C→A | 5.2% | A909A (GCG→GCT) | sslE ← | putative secreted and surface‑associated lipoprotein mucinase |
RA | 3,150,525 | C→T | 5.6% | C288C (TGC→TGT) | yghA → | putative oxidoreductase |
RA | 3,299,293 | C→A | 5.2% | P107Q (CCG→CAG) | yhbO → | stress‑resistance protein |
RA | 3,423,531 | T→G | 6.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
RA | 3,423,540 | A→G | 8.7% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
RA | 3,449,937 | G→T | 6.4% | R99R (CGC→CGA) | rplV ← | 50S ribosomal subunit protein L22 |
RA | 3,449,960 | G→T | 6.2% | R92S (CGT→AGT) | rplV ← | 50S ribosomal subunit protein L22 |
RA | 3,449,971 | C→T | 6.8% | R88H (CGT→CAT) | rplV ← | 50S ribosomal subunit protein L22 |
RA | 3,504,861 | T→A | 15.6% | intergenic (+78/+74) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
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 | 3,577,360 | C→T | 8.2% | R78H (CGC→CAC) | gntK ← | gluconate kinase 2 |
RA | 3,635,235 | T→G | 5.1% | L132R (CTG→CGG) | yhiM → | acid resistance protein, inner membrane |
RA | 3,859,354 | T→C | 48.7% | N255D (AAC→GAC) | yidK ← | putative transporter |
JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
RA | 3,894,980 | C→A | 7.8% | P110Q (CCG→CAG) | chrR → | chromate reductase, Class I, flavoprotein |
RA | 3,903,621 | G→A | 18.5% | G27G (GGC→GGT) | bglB ← | cryptic phospho‑beta‑glucosidase B |
RA | 3,907,574 | T→C | 6.9% | D2G (GAC→GGC) | phoU ← | negative regulator of PhoR/PhoB two‑component regulator |
RA | 3,909,566 | G→A | 6.0% | A278V (GCG→GTG) | pstC ← | phosphate ABC transporter permease |
RA | 3,936,327 | C→T | 7.1% | A17V (GCC→GTC) | rbsB → | D‑ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor |
RA | 4,105,496 | C→A | 6.4% | G59C (GGT→TGT) | cpxR ← | response regulator in two‑component regulatory system with CpxA |
RA | 4,171,648 | A→C | 5.7% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
RA | 4,186,578 | A→G | 89.3% | D410G (GAT→GGT) | rpoC → | RNA polymerase, beta prime subunit |
RA | 4,213,390 | C→T | 5.6% | Q53* (CAA→TAA) | yjaA → | stress‑induced protein |
RA | 4,285,364 | T→C | 12.4% | intergenic (‑151/+49) | yjcH ← / ← acs | DUF485 family inner membrane protein/acetyl‑CoA synthetase |
RA | 4,296,060 | C→T | 22.1% | 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 | 4,304,455 | C→A | 6.4% | intergenic (‑52/+157) | ytcA ← / ← yjcS | putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein |
RA | 4,329,852 | C→A | 5.2% | P165T (CCT→ACT) | yjcZ → | YjcZ family protein; yhjH motility defect suppressor |
RA | 4,385,382 | C→A | 5.5% | intergenic (+41/‑11) | yjeM → / → yjeN | putative transporter/uncharacterized protein |
RA | 4,406,129 | T→C | 92.5% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
RA | 4,407,134 | G→T | 5.6% | G161C (GGC→TGC) | rnr → | exoribonuclease R, RNase R |
RA | 4,411,493 | C→T | 5.3% | G64G (GGC→GGT) | yjfK → | DUF2491 family protein |
RA | 4,538,900 | G→A | 5.2% | T201M (ACG→ATG) | nanC ← | N‑acetylnuraminic acid outer membrane channel protein |
RA | 4,550,253 | C→T | 5.1% | V348V (GTG→GTA) | gntP ← | fructuronate transporter |
RA | 4,606,207:1 | +G | 100% | noncoding (80/87 nt) | leuP ← | tRNA‑Leu |
RA | 4,633,657 | C→T | 100% | C30Y (TGC→TAC) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
RA | 4,633,785 | C→A | 7.0% | intergenic (‑40/‑12) | yjjX ← / → ytjC | non‑canonical purine NTP phosphatase, ITPase/XTPase/phosphatase |
RA | 4,634,087 | C→A | 8.8% | T97T (ACC→ACA) | ytjC → | phosphatase |
JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 366172 | 366389 | 218 | 27 [21] | [23] 28 | [lacZ] | [lacZ] |
* | * | ÷ | NC_000913 | 773026 | 774179 | 1154 | 24 [22] | [22] 25 | [cydA]–[cydB] | [cydA],[cydB] |
* | * | ÷ | NC_000913 | 1037711 | 1039292 | 1582 | 24 [22] | [21] 26 | cbdA | cbdA |
* | * | ÷ | NC_000913 | 1166027 | 1167400 | 1374 | 24 [22] | [21] 25 | ndh | ndh |
* | * | ÷ | NC_000913 | 3423770–3424234 | 3424525–3424238 | 5–756 | 27 [21] | [20] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 290634 = | NA (NA) | 4 (0.040) | 4/256 | NT | NA | noncoding (768/768 nt) | IS1 | repeat region |
? | NC_000913 | = 3470951 | NA (NA) | coding (379/1185 nt) | tufA | translation elongation factor EF‑Tu 1 | |||||
* | ? | NC_000913 | 374922 = | NA (NA) | 13 (0.140) | 5/240 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
* | ? | NC_000913 | 374922 = | NA (NA) | 6 (0.060) +GCCA |
4/248 | NT | 6.2% | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
? | NC_000913 | = 758445 | 93 (0.910) | noncoding (37/118 nt) | RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP67 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
* | ? | NC_000913 | = 374929 | 83 (1.110) | 12 (0.180) | 7/170 | NT | 13.8% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
? | NC_000913 | = 377521 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
* | ? | NC_000913 | 374930 = | NA (NA) | 35 (0.520) | 7/170 | NT | 33.2% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
? | NC_000913 | 377522 = | 78 (1.040) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
* | ? | NC_000913 | 375124 = | 115 (1.130) | 5 (0.070) | 3/172 | NT | 6.1% | noncoding (195/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
? | NC_000913 | 377530 = | 77 (1.130) | intergenic (+219/+5) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
* | ? | NC_000913 | 566098 = | 92 (0.900) | 8 (0.090) +GAGAGGAGGATTACAAA |
7/222 | NT | 7.8% | pseudogene (279/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
? | NC_000913 | 4397412 = | 126 (1.240) | coding (1/1848 nt) | mutL | methyl‑directed mismatch repair protein | |||||
* | ? | NC_000913 | 608011 = | NA (NA) | 9 (0.090) | 6/248 | NT | NA | noncoding (5/1345 nt) | IS186 | repeat region |
? | NC_000913 | = 2515625 | NA (NA) | intergenic (+182/+18) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase | |||||
* | ? | NC_000913 | = 781016 | 53 (0.520) | 3 (0.030) | 3/220 | NT | 5.7% | intergenic (+98/‑52) | lysW/valZ | tRNA‑Lys/tRNA‑Val |
? | NC_000913 | 781653 = | 53 (0.610) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase, subunit A | |||||
* | ? | NC_000913 | 1207790 = | 38 (0.370) | 31 (0.350) | 20/224 | NT | 47.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | NC_000913 | 1209619 = | 36 (0.400) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | NC_000913 | = 1207805 | 39 (0.380) | 33 (0.370) | 16/224 | NT | 48.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | NC_000913 | = 1209602 | 36 (0.400) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 74 (0.750) | 40/248 | 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 | 4373286 = | 78 (0.950) | 55 (0.670) | 6/206 | NT | 41.4% | noncoding (90/99 nt) | RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP328 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
? | NC_000913 | 4374508 = | NA (NA) | noncoding (11/99 nt) | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
* | ? | NC_000913 | 4373296 = | 69 (0.730) | 95 (1.010) | 7/236 | NT | 58.1% | intergenic (+134/+69) | yjeI/yjeJ | DUF4156 family lipoprotein/uncharacterized protein |
? | NC_000913 | 4374498 = | NA (NA) | noncoding (1/99 nt) | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP329 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |