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 | annotation | gene | description |
| RA | 30,564 | T→C | V305A (GTA→GCA) | carA → | carbamoyl phosphate synthetase subunit alpha |
| RA | 84,230 | A→G | intergenic (‑522/‑138) | leuL ← / → leuO | leu operon leader peptide/DNA‑binding transcriptional dual regulator LeuO |
| RA | 160,139 | A→G | intergenic (‑27/+10) | gluQ ← / ← dksA | glutamyl‑Q tRNA(Asp) synthetase/RNA polymerase‑binding transcription factor DksA |
| RA | 215,896 | A→G | T210A (ACC→GCC) | nlpE → | lipoprotein NlpE |
| RA | 216,771 | A→G | V78A (GTA→GCA) | yaeF ← | peptidase C92 family protein |
| RA | 240,524 | T→C | M61T (ATG→ACG) | ivy → | periplasmic chaperone, inhibitor of vertebrate C‑type lysozyme |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 280,710 | (C)5→6 | coding (26/351 nt) | yagB ← | orphan antitoxin YagB |
| RA | 290,104 | A→G | F68L (TTT→CTT) | argF ← | CP4‑6 prophage; ornithine carbamoyltransferase ArgF |
| RA | 310,057 | (G)6→5 | intergenic (‑31/+27) | ecpB ← / ← ecpA | putative fimbrial chaperone EcpB/common pilus major subunit |
| RA | 347,389 | C→T | G352D (GGC→GAC) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| MC JC | 380,020 | (G)10→7 | intergenic (‑139/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 412,625 | A→G | S1043S (AGT→AGC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 434,614 | (C)6→8 | intergenic (+56/‑33) | ribD → / → ribE | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase/6,7‑dimethyl‑8‑ribityllumazine synthase |
| RA | 461,311 | (T)7→6 | intergenic (+69/‑140) | lon → / → hupB | Lon protease/DNA‑binding protein HU‑beta |
| RA | 489,601 | A→G | L1022L (TTA→TTG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 532,425 | C→T | intergenic (‑204/‑26) | allS ← / → allA | DNA‑binding transcriptional activator AllS/ureidoglycolate lyase |
| RA | 628,897 | A→G | N116S (AAC→AGC) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| RA | 654,659 | A→G | L437P (CTT→CCT) | dcuC ← | anaerobic C4‑dicarboxylate transporter DcuC |
| RA | 721,197 | C→T | Q179Q (CAG→CAA) | kdpE ← | DNA‑binding transcriptional activator KdpE |
| RA | 779,681 | A→G | A28A (GCA→GCG) | cpoB → | cell division coordinator CpoB |
| RA | 796,299 | A→G | L146L (TTA→TTG) | modB → | molybdate ABC transporter membrane subunit |
| RA | 858,265 | A→G | L266P (CTC→CCC) | ybiU ← | DUF1479 domain‑containing protein YbiU |
| RA | 863,794 | C→T | G51G (GGC→GGT) | fsaA → | fructose‑6‑phosphate aldolase 1 |
| RA | 868,414 | Δ1 bp | coding (895/1872 nt) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 925,008 | A→G | D582G (GAT→GGT) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 972,716 | A→G | V229A (GTC→GCC) | elyC ← | envelope biogenesis factor |
| RA | 973,477 | T→C | intergenic (‑76/‑60) | elyC ← / → cmoM | envelope biogenesis factor/tRNA cmo(5)U34 methyltransferase |
| RA | 977,613 | T→C | C430R (TGC→CGC) | mukB → | chromosome partitioning protein MukB |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,020,252 | (A)8→7 | intergenic (‑199/+158) | ompA ← / ← sulA | outer membrane porin A/cell division inhibitor SulA |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,198,069 | T→C | S57G (AGC→GGC) | ymfE ← | e14 prophage; uncharacterized protein YmfE |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,227,776 | (A)8→7 | coding (96/327 nt) | ycgL → | PF05166 family protein YcgL |
| RA | 1,238,531 | A→G | T321A (ACC→GCC) | dadA → | D‑amino acid dehydrogenase |
| RA | 1,248,546 | (T)7→6 | coding (569/1419 nt) | dhaM ← | dihydroxyacetone kinase subunit M |
| RA | 1,253,338 | T→C | D872G (GAC→GGC) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,273,675 | A→G | intergenic (‑76/‑109) | ychN ← / → ychO | DsrE/F sulfur relay family protein YchN/putative invasin YchO |
| RA | 1,280,895 | A→G | E344E (GAA→GAG) | narG → | nitrate reductase A subunit alpha |
| RA | 1,295,900 | T→C | N741S (AAC→AGC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,308,595 | C→T | W17* (TGG→TGA) | clsA ← | cardiolipin synthase A |
| RA | 1,332,663 | A→G | N539S (AAC→AGC) | topA → | DNA topoisomerase 1 |
| RA | 1,361,298 | C→T | P60L (CCG→CTG) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,364,513 | T→C | R94R (CGT→CGC) | puuB → | gamma‑glutamylputrescine oxidase |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,405,378 | A→G | D213G (GAC→GGC) | abgR → | putative LysR‑type DNA‑binding transcriptional regulator AbgR |
| RA | 1,420,378 | A→G | N5S (AAC→AGC) | ydaS → | Rac prophage; toxin YdaS |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,636,503 | 2 bp→CA | intergenic (‑136/‑252) | nohA ← / → ynfO | Qin prophage; putative prophage DNA‑packaging protein NohA/Qin prophage; protein YnfO |
| RA | 1,645,811 | (T)6→5 | coding (62/240 nt) | relB ← | Qin prophage; antitoxin/DNA‑binding transcriptional repressor RelB |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,742,590 | (G)5→4 | intergenic (+29/+11) | cfa → / ← ribC | cyclopropane fatty acyl phospholipid synthase/riboflavin synthase |
| RA | 1,825,038 | (T)7→8 | intergenic (‑101/+102) | ves ← / ← spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| RA | 1,864,197 | G→A | A116A (GCG→GCA) | yeaD → | putative aldose 1‑epimerase YeaD |
| RA | 1,866,321 | A→G | V51A (GTA→GCA) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,879,114 | T→C | T48A (ACG→GCG) | yeaQ ← | PF04226 family protein YeaQ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,895,983 | C→T | S393S (AGC→AGT) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,902,517 | G→A | G157E (GGG→GAG) | manX → | mannose‑specific PTS enzyme IIAB component |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,990,393 | G→A | G238D (GGC→GAC) | tyrP → | tyrosine:H(+) symporter |
| RA | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase FliI |
| RA | 2,018,530 | (C)6→7 | coding (145/1128 nt) | fliK → | flagellar hook‑length control protein |
| RA | 2,087,836 | C→T | G141G (GGG→GGA) | yeeY ← | putative DNA‑binding transcriptional regulator YeeY |
| RA | 2,119,480 | T→C | T227A (ACC→GCC) | wzxC ← | M‑antigen undecaprenyl disphosphate flippase |
| RA | 2,123,631 | T→C | N297S (AAC→AGC) | cpsB ← | mannose‑1‑phosphate guanylyltransferase |
| RA | 2,158,221 | G→A | G987R (GGG→AGG) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,200,454 | (A)8→7 | coding (176/3633 nt) | yehI → | DUF4132 domain‑containing protein YehI |
| RA | 2,214,473 | T→C | T58A (ACC→GCC) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,251,238 | G→A | A133A (GCG→GCA) | nfo → | endonuclease IV |
| RA | 2,297,114 | (C)7→8 | coding (531/624 nt) | ccmA ← | heme trafficking system ATP‑binding protein |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,402,585 | T→C | T421A (ACT→GCT) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,402,681 | A→C | S389A (TCT→GCT) | nuoC ← | NADH:quinone oxidoreductase subunit CD |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,498,786 | C→T | A39V (GCG→GTG) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,521,306 | T→C | noncoding (54/76 nt) | lysV → | tRNA‑Lys |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,541,837 | T→C | T226A (ACG→GCG) | cysU ← | sulfate/thiosulfate ABC transporter inner membrane subunit CysU |
| RA | 2,548,769 | T→C | L223P (CTT→CCT) | yfeW → | penicillin binding protein 4B |
| RA | 2,581,382 | C→T | P583S (CCC→TCC) | tktB → | transketolase 2 |
| RA | 2,612,831 | T→C | V311A (GTT→GCT) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,649,765 | Δ1 bp | coding (2523/4962 nt) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,660,213 | T→C | N26S (AAC→AGC) | iscU ← | scaffold protein for iron‑sulfur cluster assembly |
| RA | 2,765,794 | (C)7→8 | intergenic (‑18/‑124) | yfjM ← / → rnlA | CP4‑57 prophage; protein YfjM/CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system |
| RA | 2,789,477 | T→C | Y165H (TAT→CAT) | csiD → | PF08943 family protein CsiD |
| RA | 2,807,920 | A→G | K263K (AAA→AAG) | proX → | glycine betaine ABC transporter periplasmic binding protein ProX |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,848,580 | G→A | A221V (GCA→GTA) | hycC ← | formate hydrogenlyase subunit HycC |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,957,414 | (T)6→5 | coding (1471/2889 nt) | ptrA ← | protease 3 |
| RA | 2,971,832 | G→A | R79H (CGC→CAC) | tas → | putative NADP(H)‑dependent aldo‑keto reductase Tas |
| RA | 2,984,223 | T→C | intergenic (‑99/+188) | kduI ← / ← yqeF | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase/putative acyltransferase |
| RA | 3,013,537 | T→C | T235A (ACG→GCG) | yqeB ← | XdhC‑CoxI family protein YqeB |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,101,039 | (C)7→8 | coding (585/720 nt) | yggN ← | putative EcfF |
| RA | 3,104,044 | A→G | L344L (TTA→TTG) | mutY → | adenine DNA glycosylase |
| RA | 3,108,163 | T→C | E331E (GAA→GAG) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,116,591 | G→A | A841V (GCC→GTC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,127,466 | T→C | T186A (ACG→GCG) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,150,701 | G→A | intergenic (+155/+117) | yghA → / ← exbD | NADP(+)‑dependent aldehyde reductase/Ton complex subunit ExbD |
| RA | 3,162,515 | A→G | V52A (GTA→GCA) | ftsP ← | cell division protein required during stress conditions |
| RA | 3,178,093 | T→C | intergenic (‑183/‑22) | nudF ← / → tolC | ADP‑sugar pyrophosphatase/outer membrane channel TolC |
| RA | 3,248,921 | A→G | intergenic (+99/‑48) | mzrA → / → yqjC | modulator protein MzrA/DUF1090 domain‑containing protein YqjC |
| RA | 3,268,419 | T→C | F2S (TTC→TCC) | yhaC → | uncharacterized protein YhaC |
| RA | 3,307,431 | T→C | T144A (ACT→GCT) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | 3,314,929 | G→A | G362G (GGC→GGT) | infB ← | translation initiation factor IF‑2 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,359,183 | T→C | *1487Q (TAA→CAA) | gltB → | glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,402,245 | A→G | V363A (GTA→GCA) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,420,861 | T→C | V243A (GTC→GCC) | yhdX → | putative ABC transporter membrane subunit YhdX |
| RA | 3,432,994 | (C)6→7 | coding (567/1125 nt) | smf ← | protein Smf |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,623,834 | G→A | intergenic (+52/‑544) | yhhH → / → yhhI | PF15631 family protein YhhH/putative transposase |
| RA | 3,780,149 | T→C | V108A (GTT→GCT) | lldD → | L‑lactate dehydrogenase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,865,527 | A→G | D249D (GAT→GAC) | yidE ← | putative transport protein YidE |
| RA | 3,898,577 | G→A | G186S (GGC→AGC) | cbrC → | UPF0167 family colicin E2 tolerance protein CbrC |
| RA | 3,904,456 | T→C | Y381C (TAC→TGC) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| JC JC | 3,923,012 | IS5 (–) +4 bp | intergenic (‑572/+42) | atpI ← / ← rsmG | ATP synthase accessory factor/16S rRNA m(7)G527 methyltransferase |
| RA | 3,934,717 | C→T | H314Y (CAT→TAT) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 3,984,869 | T→C | E380G (GAA→GGA) | aslA ← | arylsulfatase |
| RA | 4,034,244 | A→G | N367S (AAC→AGC) | trkH → | K(+) transporter TrkH |
| RA | 4,177,879 | C→T | T46I (ACC→ATC) | nusG → | transcription termination factor NusG |
| RA | 4,178,045 | G→A | A101A (GCG→GCA) | nusG → | transcription termination factor NusG |
| RA | 4,198,636 | A→G | E307E (GAA→GAG) | hemE → | uroporphyrinogen decarboxylase |
| RA | 4,200,155 | (C)6→5 | intergenic (+61/‑126) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,224,381 | A→G | D185G (GAC→GGC) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,416,367 | C→T | intergenic (‑75/+74) | yjfN ← / ← bsmA | protease activator/DUF1471 domain‑containing putative lipoprotein BsmA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,535,174 | A→G | pseudogene (160/1017 nt) | yjhR → | KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR |
| RA | 4,548,789 | A→G | intergenic (+1/‑19) | fimG → / → fimH | type 1 fimbriae minor subunit FimG/type 1 fimbriae D‑mannose specific adhesin |
| RA | 4,586,594 | (G)6→7 | coding (168/3513 nt) | hsdR ← | type I restriction enzyme EcoKI endonuclease component |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,382 | A→G | noncoding (20/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1636161–1636361 | 1636484 | 124–324 | 25 [23] | [22] 26 | [nohA] | [nohA] |
| * | * | ÷ | NC_000913 | 3423755–3424233 | 3424523–3424239 | 7–769 | 27 [23] | [20] 33 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 14 (0.160) | 100 (1.300) | 58/244 | 0.1 | 89.9% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 10 (0.130) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 14 (0.160) | 74 (0.960) | 46/244 | 0.4 | 86.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 10 (0.130) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 133 (1.520) | 151 (1.740) | 76/274 | 0.0 | 69.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 3 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 84 (0.960) | 52/276 | 0.4 | 90.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.100) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||