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 | 7,890 | C→T | A24T (GCA→ACA) | yaaJ ← | putative transporter YaaJ |
| RA | 35,173 | A→G | Y67H (TAC→CAC) | caiE ← | putative transferase CaiE |
| RA | 48,716 | A→G | R316R (CGA→CGG) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 59,087 | T→C | L205P (CTA→CCA) | yabP → | putative uncharacterized protein YabP |
| RA | 68,452 | C→T | E533K (GAA→AAA) | araB ← | ribulokinase |
| RA | 132,169 | A→G | A185A (GCA→GCG) | acnB → | hypothetical protein |
| RA | 207,792 | C→T | D889D (GAC→GAT) | dnaE → | DNA polymerase III subunit alpha |
| RA | 215,141 | (A)8→9 | coding (309/423 nt) | arfB → | peptidyl‑tRNA hydrolase, ribosome rescue factor |
| RA | 226,266 | A→G | noncoding (508/2904 nt) | rrlH → | 23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 277,026 | A→G | E104E (GAA→GAG) | mmuM → | homocysteine S‑methyltransferase |
| RA | 282,735 | T→C | V153A (GTG→GCG) | yagE → | CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 294,167 | A→G | A211A (GCT→GCC) | yagM ← | CP4‑6 prophage; protein YagM |
| RA | 339,343 | C→T | P340L (CCG→CTG) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 372,078 | G→A | L280L (CTG→CTA) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 406,920 | C→T | I172I (ATC→ATT) | aroL → | shikimate kinase 2 |
| RA | 415,480 | A→G | Y92H (TAC→CAC) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 451,526 | G→A | L29L (CTG→TTG) | cyoA ← | cytochrome bo3 ubiquinol oxidase subunit 2 |
| RA | 456,274 | C→T | P381L (CCG→CTG) | tig → | trigger factor |
| RA | 481,275 | G→A | S1043S (AGC→AGT) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 511,672 | T→C | V11A (GTG→GCG) | glsA → | glutaminase 1 |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 592,834 | A→G | R115R (CGT→CGC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 608,093 | C→T | A10V (GCA→GTA) | insL‑2 → | IS186/IS421 transposase |
| RA | 693,466 | C→T | intergenic (‑88/+65) | ybeZ ← / ← miaB | PhoH‑like protein/isopentenyl‑adenosine A37 tRNA methylthiolase |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | sensory histidine kinase KdpD |
| RA | 776,687 | C→T | Q116* (CAG→TAG) | tolA → | Tol‑Pal system protein TolA |
| RA | 780,986 | A→G | intergenic (+68/‑82) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 865,679 | T→A | D229V (GAT→GTT) | moeA ← | molybdopterin molybdotransferase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 950,062 | A→G | D132G (GAC→GGC) | ycaK → | putative NAD(P)H‑dependent oxidoreductase YcaK |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,024,384 | G→A | intergenic (‑36/‑87) | yccF ← / → helD | conserved inner membrane protein YccF/DNA helicase IV |
| RA | 1,093,358 | (G)6→7 | coding (483/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,128,342 | C→T | N168N (AAC→AAT) | murJ → | putative lipid II flippase MurJ |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,184,398 | G→A | P16L (CCC→CTC) | potB ← | spermidine preferential ABC transporter membrane subunit PotB |
| RA | 1,212,088 | (C)8→7 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
| RA | 1,220,492 | (T)7→8 | pseudogene (892/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,223,948 | A→G | intergenic (+41/+331) | ycgI → / ← minE | protein YcgI/Z‑ring positioning protein MinE |
| RA | 1,241,484 | A→G | G196G (GGT→GGC) | cvrA ← | putative K(+):H(+) antiporter |
| RA | 1,248,684 | A→G | I144T (ATC→ACC) | dhaM ← | dihydroxyacetone kinase subunit M |
| RA | 1,283,325 | T→C | R1154R (CGT→CGC) | narG → | nitrate reductase A subunit alpha |
| RA | 1,287,152 | T→C | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
small RNA RttR protamine‑like protein |
| RA | 1,287,161 | G→A | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
small RNA RttR protamine‑like protein |
| RA | 1,295,607 | C→T | D839N (GAC→AAC) | adhE ← | aldehyde‑alcohol dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,332,839 | G→A | D598N (GAC→AAC) | topA → | DNA topoisomerase 1 |
| RA | 1,371,377 | A→G | M388V (ATG→GTG) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,398,338 | A→G | R95R (CGT→CGC) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,420,539 | C→T | L59L (CTG→TTG) | ydaS → | Rac prophage; toxin YdaS |
| RA | 1,423,030 | A→G | P93P (CCA→CCG) | ydaW → | Rac prophage; putative uncharacterized protein YdaW |
| RA | 1,466,474 | T→C | pseudogene (1083/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,483,525 | T→C | G155G (GGT→GGC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,587,425 | T→C | T104A (ACC→GCC) | ydeQ ← | putative fimbrial adhesin protein YdeQ |
| RA | 1,623,117 | A→G | I245T (ATC→ACC) | dgcZ ← | diguanylate cyclase DgcZ |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,656,365 | T→C | V61A (GTG→GCG) | speG → | spermidine N‑acetyltransferase |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,716,441 | A→T | I261N (ATC→AAC) | tyrS ← | tyrosine‑‑tRNA ligase |
| RA | 1,720,383 | (C)5→6 | intergenic (+40/+7) | slyB → / ← slyA | outer membrane lipoprotein SlyB/DNA‑binding transcriptional dual regulator SlyA |
| RA | 1,744,008 | T→C | G184G (GGT→GGC) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,768,131 | (C)6→7 | coding (555/3057 nt) | ydiJ ← | putative FAD‑linked oxidoreductase |
| RA | 1,808,958 | G→A | F92F (TTC→TTT) | yniB ← | uncharacterized protein YniB |
| RA | 1,826,277 | G→A | P216L (CCC→CTC) | astE ← | succinylglutamate desuccinylase |
| RA | 1,833,210 | (C)5→6 | coding (783/807 nt) | xthA → | exodeoxyribonuclease III |
| RA | 1,838,177 | Δ1 bp | coding (966/1536 nt) | ynjC → | putative ABC transporter membrane subunit YnjC |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,893,650 | T→C | V95A (GTA→GCA) | yoaB → | RutC family protein YoaB |
| RA | 1,969,962 | A→G | S341S (AGT→AGC) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,988,066 | C→T | intergenic (‑107/‑156) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 2,012,563 | (G)6→8 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,061,676 | A→G | G86G (GGT→GGC) | nac ← | DNA‑binding transcriptional dual regulator Nac |
| RA | 2,128,386 | (C)5→6 | coding (503/549 nt) | wcaF ← | putative acyl transferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,178,044 | T→C | E174G (GAG→GGG) | fbaB ← | fructose‑bisphosphate aldolase class I |
| RA | 2,217,485 | A→G | V358A (GTG→GCG) | yehY ← | glycine betaine ABC transporter membrane subunit YehY |
| RA | 2,221,754 | G→A | A79V (GCG→GTG) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,229,799 | G→A | P196L (CCG→CTG) | dusC ← | tRNA‑dihydrouridine(16) synthase |
| RA | 2,258,752 | T→C | H182R (CAC→CGC) | psuK ← | putative pseudouridine kinase |
| RA | 2,305,396 | (C)5→6 | coding (1359/1647 nt) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,336,956 | A→G | V822A (GTG→GCG) | gyrA ← | DNA gyrase subunit A |
| RA | 2,388,168 | T→C | I87V (ATT→GTT) | yfbN ← | uncharacterized protein YfbN |
| RA | 2,421,435 | G→A | T37T (ACG→ACA) | folX → | dihydroneopterin triphosphate 2'‑epimerase |
| 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 | 2,486,481 | (A)7→8 | coding (2108/3594 nt) | evgS → | sensory histidine kinase EvgS |
| RA | 2,500,067 | T→C | V466A (GTC→GCC) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,515,903 | T→C | T644A (ACC→GCC) | pdeA ← | putative c‑di‑GMP phosphodiesterase PdeA |
| RA | 2,524,341 | C→T | G180S (GGT→AGT) | xapA ← | xanthosine phosphorylase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,584,855 | G→A | A224V (GCC→GTC) | aegA ← | putative oxidoreductase Fe‑S subunit AegA |
| RA | 2,638,200 | T→C | A151A (GCA→GCG) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,680,086 | G→A | T887I (ACC→ATC) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,695,282 | A→G | S88P (TCT→CCT) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,717,078 | G→A | G109S (GGT→AGT) | ung → | uracil‑DNA glycosylase |
| RA | 2,749,328 | T→C | I185I (ATT→ATC) | yfjD → | putative inner membrane protein |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,816,592 | (A)8→9 | coding (349/429 nt) | yqaA ← | DedA family protein YqaA |
| RA | 2,826,032 | T→C | R67R (CGT→CGC) | srlA → | sorbitol‑specific PTS enzyme IIC2 component |
| RA | 2,836,321 | C→T | E369K (GAA→AAA) | hypF ← | carbamoyltransferase HypF |
| 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 | 3,017,209 | A→G | T384A (ACT→GCT) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,023,591 | A→G | E759G (GAG→GGG) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,144,028 | T→C | N46S (AAC→AGC) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,153,311 | G→A | R359H (CGC→CAC) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase |
| RA | 3,174,590 | G→A | N269N (AAC→AAT) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,208,470 | G→A | L149L (CTG→CTA) | ttdT → | L‑tartrate:succinate antiporter |
| RA | 3,221,527 | T→C | V21A (GTC→GCC) | ebgR → | DNA‑binding transcriptional repressor EbgR |
| RA | 3,233,438 | A→T | I592F (ATC→TTC) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,253,203 | (T)7→8 | coding (293/357 nt) | yhaI → | putative inner membrane protein |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,311,376 | (A)6→7 | noncoding (194/216 nt) | sraG → | small regulatory RNA SraG |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,354,613 | (G)5→6 | intergenic (‑563/‑112) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,369,083 | T→C | G132G (GGA→GGG) | yhcH ← | DUF386 domain‑containing protein YhcH |
| RA | 3,379,266 | (C)7→8 | coding (732/1128 nt) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,401,922 | G→A | L471L (CTA→TTA) | csrD ← | regulator of CsrB and CsrC decay |
| RA | 3,429,507 | A→G | H91R (CAC→CGC) | yrdA → | protein YrdA |
| RA | 3,437,370 | T→C | S285P (TCG→CCG) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,522,713 | T→C | Q13Q (CAA→CAG) | hofM ← | DNA utilization protein HofM |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,641,125 | A→G | A88A (GCA→GCG) | dtpB → | dipeptide/tripeptide:H(+) symporter DtpB |
| RA | 3,727,102 | A→G | V87A (GTT→GCT) | yiaA ← | conserved inner membrane protein YiaA |
| RA | 3,730,668 | A→G | V33A (GTG→GCG) | xylA ← | xylose isomerase |
| RA | 3,768,992 | A→G | intergenic (+102/‑353) | yibS → / → yibV | RHS family protein YibS/PF15596 family protein YibV |
| 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 | 3,876,104 | G→A | intergenic (+10/+36) | yidX → / ← yidA | putative lipoprotein YidX/sugar phosphatase YidA |
| RA | 3,884,028 | G→A | M1M (ATG→ATA) † | ysdD → | protein YsdD |
| RA | 3,932,381 | A→G | S356G (AGC→GGC) | kup → | K(+):H(+) symporter Kup |
| RA | 4,043,500 | A→G | Y28C (TAC→TGC) | dsbA → | thiol:disulfide oxidoreductase DsbA |
| RA | 4,056,347 | T→C | intergenic (‑8/+278) | glnL ← / ← glnA | sensory histidine kinase NtrB/glutamine synthetase |
| RA | 4,103,091 | C→T | T90T (ACC→ACT) | yiiM → | 2‑amino‑6‑N‑hydroxylaminopurine resistance protein |
| RA | 4,162,672 | A→G | L200P (CTG→CCG) | trmA ← | tRNA m(5)U54 methyltransferase |
| RA | 4,276,188 | (T)5→4 | coding (718/1587 nt) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,329,894 | (G)6→7 | coding (535/879 nt) | yjcZ → | uncharacterized protein YjcZ |
| RA | 4,381,680 | A→G | G213G (GGT→GGC) | frdA ← | fumarate reductase flavoprotein subunit |
| RA | 4,395,850 | A→G | E89G (GAG→GGG) | tsaE → | N(6)‑L‑threonylcarbamoyladenine synthase, TsaE subunit |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,423,357 | A→G | Y171C (TAC→TGC) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,560,919 | A→G | intergenic (‑239/‑11) | yjiH ← / → kptA | Gate family protein YjiH/RNA 2'‑phosphotransferase |
| RA | 4,567,117 | C→T | A44T (GCT→ACT) | yjiN ← | DUF445 domain‑containing protein YjiN |
| RA | 4,588,797 | A→G | H23H (CAT→CAC) | yjiA ← | P‑loop guanosine triphosphatase |
| RA | 4,589,321 | A→G | N653N (AAT→AAC) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,604,679 | G→A | A174T (GCC→ACC) | bglJ → | DNA‑binding transcriptional regulator BglJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 270640–271294 | 271646–271587 | 294–1007 | 10 [8] | [7] 11 | insI‑1 | IS30 transposase |
| * | * | ÷ | NC_000913 | 1286922 | 1287143 | 222 | 10 [9] | [7] 10 | [ychS]–[tpr] | [ychS],[rttR],[tpr] |
| * | * | ÷ | NC_000913 | 3423785–3424231 | 3424525–3424239 | 9–741 | 10 [8] | [6] 10 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 59 (1.250) | 61 (1.300) | 38/274 | 0.2 | 67.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 58 (1.230) | 43/276 | 0.1 | 98.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 30 (0.640) | 12 (0.270) | 11/258 | 2.3 | 24.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 45 (1.020) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 30 (0.640) | 11 (0.250) | 10/258 | 2.5 | 23.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 45 (1.020) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||