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 | 15,231 | A→G | H355R (CAC→CGC) | dnaJ → | chaperone protein DnaJ |
| RA | 55,489 | A→G | F541L (TTC→CTC) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 73,670 | A→G | R284R (CGT→CGC) | thiP ← | thiamine ABC transporter membrane subunit |
| RA | 107,553 | (T)9→8 | intergenic (+79/‑152) | lpxC → / → secM | UDP‑3‑O‑acyl‑N‑acetylglucosamine deacetylase/SecA translation regulator |
| RA | 129,270 | C→T | G453G (GGC→GGT) | lpd → | lipoamide dehydrogenase |
| RA | 179,722 | A→G | L162L (TTA→TTG) | dgt → | dGTP triphosphohydrolase |
| RA | 233,193 | C→T | D255N (GAT→AAT) | mltD ← | membrane‑bound lytic murein transglycosylase D |
| RA | 244,295 | (G)5→6 | intergenic (+174/‑32) | lpcA → / → yafJ | D‑sedoheptulose 7‑phosphate isomerase/putative amidotransferase |
| RA | 246,808 | T→C | S33P (TCT→CCT) | yafL → | NlpC/P60 family protein YafL |
| RA | 250,190 | C→T | pseudogene (119/756 nt) | lafU → | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 263,792 | A→G | H72H (CAT→CAC) | yafW ← | antitoxin of the YkfI‑YafW toxin‑antitoxin pair |
| RA | 271,958 | C→T | pseudogene (195/427 nt) | insN → | CP4‑6 prophage; IS911A regulator fragment |
| RA | 347,492 | C→T | A318T (GCC→ACC) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 363,003 | G→A | F59F (TTC→TTT) | lacY ← | lactose permease |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 570,833 | G→A | intergenic (+405/‑60) | ybcK → / → ybcL | DLP12 prophage; putative recombinase/DLP12 prophage; periplasmic protein YbcL |
| RA | 572,368 | A→G | M1M (ATG→GTG) † | ylcH → | DLP12 prophage; uncharacterized protein YlcH |
| RA | 581,442 | C→T | pseudogene (89/309 nt) | aaaD → | DLP12 prophage; protein AaaD |
| RA | 603,108 | A→G | M384V (ATG→GTG) | pheP → | phenylalanine:H(+) symporter PheP |
| RA | 615,673 | A→G | D506G (GAC→GGC) | entF → | apo‑serine activating enzyme |
| RA | 672,440 | T→C | I782V (ATC→GTC) | leuS ← | leucine‑‑tRNA ligase |
| RA | 722,937 | T→C | N493S (AAC→AGC) | kdpD ← | sensory histidine kinase KdpD |
| RA | 868,422 | (C)8→7 | coding (903/1872 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 | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 951,980 | A→G | C525C (TGT→TGC) | pflB ← | pyruvate formate‑lyase |
| 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 | 1,038,554 | T→C | V272A (GTT→GCT) | appC → | cytochrome bd‑II ubiquinol oxidase subunit I |
| RA | 1,042,861 | A→G | R450R (CGT→CGC) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,074,478 | A→G | A79A (GCA→GCG) | rutR → | DNA‑binding transcriptional dual regulator RutR |
| RA | 1,075,403 | A→G | C1160C (TGT→TGC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,118,667 | A→G | V127A (GTC→GCC) | yceJ ← | putative cytochrome b561 |
| RA | 1,122,640 | (T)5→4 | intergenic (‑33/+73) | pyrC ← / ← yceB | dihydroorotase/putative lipid‑binding lipoprotein YceB |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,199,214 | A→G | T174A (ACA→GCA) | lit → | e14 prophage; cell death peptidase Lit |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,274,477 | A→G | T232A (ACA→GCA) | ychO → | putative invasin YchO |
| RA | 1,287,009 | A→T | intergenic (+25/+57) | ychS → / ← rttR | putative uncharacterized protein YchS/small RNA RttR |
| RA | 1,292,182 | C→T | T242T (ACC→ACT) | galU → | UTP‑‑glucose‑1‑phosphate uridylyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,318,581 | A→G | V403A (GTT→GCT) | trpC ← | fused indole‑3‑glycerol phosphate synthase/phosphoribosylanthranilate isomerase |
| RA | 1,348,715 | A→G | S66S (AGT→AGC) | rnb ← | RNase II |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,393,412 | T→C | I62I (ATT→ATC) | mppA → | murein tripeptide ABC transporter periplasmic binding protein |
| RA | 1,482,477 | A→G | G128G (GGT→GGC) | azoR ← | FMN dependent NADH:quinone oxidoreductase |
| RA | 1,523,635 | A→C | N110T (AAC→ACC) | yncE → | PQQ‑like domain‑containing protein YncE |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,583,445 | A→G | A81A (GCT→GCC) | ydeO ← | DNA‑binding transcriptional dual regulator YdeO |
| RA | 1,594,132 | (C)8→7 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,603,730 | A→G | T238A (ACC→GCC) | lsrC → | Autoinducer‑2 ABC transporter membrane subunit LsrC |
| RA | 1,627,973 | T→C | F153L (TTT→CTT) | ydfG → | 3‑hydroxy acid dehydrogenase |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,640,492 | T→C | T32A (ACT→GCT) | essQ ← | Qin prophage; putative S lysis protein |
| RA | 1,650,215 | A→G | pseudogene (138/921 nt) | ydfE → | Qin prophage; protein YdfE |
| RA | 1,680,476 | T→C | V307A (GTA→GCA) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,680,494 | C→T | T313I (ACT→ATT) | ydgI → | putative arginine:ornithine antiporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
| RA | 1,775,461 | G→A | intergenic (+17/‑126) | aroD → / → ydiF | 3‑dehydroquinate dehydratase/putative acetate‑CoA transferase |
| RA | 1,788,645 | T→C | Y71H (TAC→CAC) | aroH → | 3‑deoxy‑7‑phosphoheptulonate synthase, Trp‑sensitive |
| RA | 1,797,060 | C→T | A295A (GCG→GCA) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,842,809 | (T)5→6 | coding (439/1344 nt) | gdhA → | glutamate dehydrogenase |
| RA | 1,853,409 | A→G | F191L (TTT→CTT) | ydjE ← | putative transporter YdjE |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,875,472 | T→C | V35V (GTA→GTG) | nimR ← | DNA‑binding transcriptional repressor NimR |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,915,076 | T→C | E153E (GAA→GAG) | proQ ← | RNA chaperone ProQ |
| RA | 1,923,946 | (G)6→7 | coding (646/873 nt) | yebZ ← | putative inner membrane protein |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,148,062 | T→C | V130A (GTC→GCC) | yegD → | HSP70 family protein YegD |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,250,657 | C→A | A314E (GCG→GAG) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,294,874 | A→G | C11R (TGC→CGC) | ccmF ← | holocytochrome c synthetase membrane subunit CcmF |
| RA | 2,326,966 | C→T | P286P (CCC→CCT) | atoB → | acetyl‑CoA acetyltransferase |
| RA | 2,331,149 | C→A | pseudogene (3254/4605 nt) | yfaS ← | putative macroglobulin family protein, N‑terminal fragment |
| RA | 2,367,550 | T→C | G160G (GGT→GGC) | arnC → | undecaprenyl‑phosphate 4‑deoxy‑4‑formamido‑L‑arabinose transferase |
| RA | 2,408,070 | T→C | R170R (CGT→CGC) | alaA → | glutamate‑‑pyruvate aminotransferase AlaA |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,549,919 | T→C | E209E (GAA→GAG) | yfeX ← | porphyrinogen peroxidase |
| RA | 2,573,760 | G→A | L182L (CTC→CTT) | eutT ← | putative ethanolamine utilization cobalamin adenosyltransferase |
| RA | 2,613,481 | T→C | L528L (TTA→CTA) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,645,263 | G→A | A688V (GCC→GTC) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,682,614 | G→A | G44G (GGC→GGT) | yphG ← | DUF5107 domain‑containing protein YphG |
| RA | 2,723,976 | A→G | H417R (CAC→CGC) | pssA → | phosphatidylserine synthase |
| RA | 2,725,583 | G→A | S55F (TCC→TTC) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,735,777 | G→A | P79S (CCG→TCG) | rluD ← | 23S rRNA pseudouridine(1911/1915/1917) synthase |
| RA | 2,749,090 | T→C | L106P (CTG→CCG) | yfjD → | putative inner membrane protein |
| RA | 2,763,601 | T→C | Y518C (TAT→TGT) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,805,910 | G→A | A366T (GCA→ACA) | proV → | glycine betaine ABC transporter ATP binding subunit ProV |
| RA | 2,810,405 | A→G | Y21C (TAT→TGT) | ygaH → | L‑valine exporter subunit YgaH |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,816,960 | C→T | A182T (GCC→ACC) | yqaB ← | fructose‑1‑phosphatase |
| RA | 2,836,245 | A→G | V394A (GTG→GCG) | hypF ← | carbamoyltransferase HypF |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,860,176 | A→G | A139A (GCA→GCG) | pphB → | phosphoprotein phosphatase 2 |
| RA | 2,949,313 | G→A | R24R (CGG→CGA) | argA → | N‑acetylglutamate synthase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,966,455 | T→C | I660M (ATA→ATG) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,985,260 | G→A | I111I (ATC→ATT) | yqeF ← | putative acyltransferase |
| RA | 2,990,923 | (C)6→7 | pseudogene (370/490 nt) | ygeF → | protein YgeF |
| RA | 2,993,641 | A→G | T2A (ACT→GCT) | ygeI → | protein YgeI |
| RA | 3,004,250 | T→C | T513A (ACG→GCG) | ygeV ← | putative sigma(54)‑dependent transcriptional regulator YgeV |
| RA | 3,062,332 | G→A | A495T (GCC→ACC) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,080,959 | C→T | R226H (CGC→CAC) | tktA ← | transketolase 1 |
| RA | 3,097,200 | Δ1 bp | coding (520/594 nt) | rdgB → | dITP/XTP pyrophosphatase |
| RA | 3,119,580 | C→T | intergenic (‑468/+17) | yghJ ← / ← glcA | putative lipoprotein YghJ/glycolate/lactate:H(+) symporter GlcA |
| RA | 3,141,198 | T→C | Y30C (TAC→TGC) | hybD ← | putative hydrogenase 2 maturation protease |
| RA | 3,194,843 | (G)6→7 | noncoding (23/145 nt) | sibD ← | small RNA SibD |
| RA | 3,216,058 | A→G | V145A (GTC→GCC) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,305,794 | T→C | Q8Q (CAA→CAG) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,538,415 | T→C | V344A (GTG→GCG) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,624,467 | A→G | L30L (CTA→CTG) | yhhI → | putative transposase |
| RA | 3,645,060 | T→C | V41V (GTA→GTG) | prlC ← | oligopeptidase A |
| RA | 3,733,737 | G→A | V513I (GTC→ATC) P6P (CCG→CCA) |
xylG → xylH → |
xylose ABC transporter ATP binding subunit xylose ABC transporter membrane subunit |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,851,355 | A→G | V477A (GTG→GCG) | ilvB ← | acetohydroxy acid synthase I subunit IlvB |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,911,170 | A→G | V119A (GTG→GCG) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,275,076 | A→G | intergenic (‑35/‑395) | yjcB ← / → pdeC | uncharacterized protein YjcB/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 | 4,301,007 | A→G | R8R (CGT→CGC) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,306,037 | A→G | G187G (GGT→GGC) | yjcS ← | alkyl sulfatase |
| RA | 4,401,790 | A→G | P373P (CCA→CCG) | hflX → | ribosome rescue factor HflX |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,462,323 | A→G | L113S (TTA→TCA) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,546,758 | A→G | T555A (ACG→GCG) | fimD → | type I fimbriae usher protein |
| RA | 4,596,427 | A→G | E146E (GAA→GAG) | lgoD → | L‑galactonate oxidoreductase |
| RA | 4,606,316 | G→A | noncoding (86/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,637,743 | (A)9→8 | coding (1048/1425 nt) | creC → | sensory histidine kinase CreC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1465105 | 1465283 | 179 | 15 [14] | [13] 15 | ynbG | ynbG |
| * | * | ÷ | NC_000913 | 2033815 | 2033963 | 149 | 15 [5] | [14] 16 | rseX/yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 3423780–3424234 | 3424525–3424238 | 5–746 | 15 [14] | [13] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3455424 | 3455523 | 100 | 16 [11] | [14] 15 | gspA/gspC | Type II secretion system protein GspA/Type II secretion system protein GspC |
| * | * | ÷ | NC_000913 | 3499389 | 3499441 | 53 | 20 [13] | [13] 15 | cysG/yhfL | siroheme synthase/DUF4223 domain‑containing lipoprotein YhfL |
| * | * | ÷ | NC_000913 | 3751932 | 3751994 | 63 | 15 [12] | [13] 15 | [yiaU] | [yiaU] |
| * | * | ÷ | NC_000913 | 4304468 | 4304635 | 168 | 15 [14] | [14] 17 | [yjcS] | [yjcS] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 69 (1.110) | 19 (0.340) | 18/244 | 1.7 | 24.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 57 (1.030) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 98 (1.570) | 82 (1.320) | 49/274 | 0.2 | 62.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 50 (0.800) | 36/276 | 0.6 | 98.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||