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 | 11,496 | C→T | W97* (TGG→TGA) | yaaI ← | hypothetical protein |
| RA | 28,419 | C→T | R16C (CGT→TGT) | dapB → | dihydrodipicolinate reductase |
| RA | 30,387 | C→T | A246V (GCC→GTC) | carA → | carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| RA | 49,463 | C→T | T565T (ACC→ACT) | kefC → | potassium:proton antiporter |
| RA | 51,338 | +G | coding (269/378 nt) | apaG ← | protein associated with Co2+ and Mg2+ efflux |
| RA | 55,008 | C→T | G701E (GGG→GAG) | imp ← | exported protein required for envelope biosynthesis and integrity |
| RA | 104,666 | A→G | T229A (ACT→GCT) | ftsA → | ATP‑binding cell division protein involved in recruitment of FtsK to Z ring |
| RA | 124,632 | A→G | Y539C (TAC→TGC) | aceE → | pyruvate dehydrogenase, decarboxylase component E1, thiamin‑binding |
| RA | 149,558 | (T)8→9 | coding (44/795 nt) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| RA | 167,651 | (G)5→6 | coding (168/2244 nt) | fhuA → | ferrichrome outer membrane transporter |
| RA | 169,953 | G→A | R59H (CGT→CAT) | fhuC → | iron‑hydroxamate transporter subunit |
| RA | 251,759 | (G)5→6 | coding (862/1056 nt) | dinB → | DNA polymerase IV |
| RA | 366,525 | A→G | S70S (AGT→AGC) | lacI ← | DNA‑binding transcriptional repressor |
| RA | 393,476 | G→A | G413D (GGC→GAC) | yaiU → | hypothetical protein |
| RA | 395,812 | C→T | intergenic (‑301/‑51) | ampH ← / → sbmA | beta‑lactamase/D‑alanine carboxypeptidase/predicted transporter |
| RA | 457,230 | A→G | D194G (GAC→GGC) | clpX → | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| RA | 483,561 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 486,032 | A→G | L91L (CTA→CTG) | kefA → | fused mechanosensitive channel proteins |
| RA | 506,176 | A→G | V44A (GTC→GCC) | ybaK ← | hypothetical protein |
| RA | 526,302 | (G)6→7 | coding (3818/4281 nt) | rhsD → | rhsD element protein |
| RA | 547,694 | A→G | intergenic (+123/‑1156) | fdrA → / → ylbF | predicted acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein |
| RA | 547,835 | +G | intergenic (+264/‑1015) | fdrA → / → ylbF | predicted acyl‑CoA synthetase with NAD(P)‑binding Rossmann‑fold domain/hypothetical protein |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 565,784 | T→C | intergenic (‑200/‑272) | ybcC ← / → insE | predicted exonuclease/IS3 element protein InsE |
| MC JC | 654,214 | Δ1,199 bp | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 706,394 | (T)9→8 | intergenic (+82/‑121) | nagE → / → glnS | fused N‑acetyl glucosamine specific PTS enzyme IICBA components/glutamyl‑tRNA synthetase |
| RA | 721,062 | C→T | intergenic (‑180/+416) | speF ← / ← kdpE | ornithine decarboxylase isozyme, inducible/DNA‑binding response regulator in two‑component regulatory system with KdpD |
| RA | 737,655 | A→G | intergenic (+534/‑859) | ybfQ → / → ybfD | predicted transposase/hypothetical protein |
| RA | 768,787 | A→G | M130V (ATG→GTG) | mngB → | alpha‑mannosidase |
| RA | 778,483 | C→T | P108S (CCG→TCG) | tolB → | periplasmic protein |
| RA | 805,405 | A→G | Y494C (TAC→TGC) | ybhJ → | predicted hydratase |
| RA | 840,393 | A→G | Y521H (TAT→CAT) | fiu ← | predicted iron outer membrane transporter |
| RA | 885,798 | A→G | R252R (CGT→CGC) | ybjI ← | hypothetical protein |
| RA | 901,267 | (C)6→7 | intergenic (‑270/+21) | artJ ← / ← artM | arginine transporter subunit/arginine transporter subunit |
| RA | 962,866 | A→G | K150K (AAA→AAG) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 963,361 | C→G | N315K (AAC→AAG) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,045,186 | A→G | L347P (CTG→CCG) | yccZ ← | predicted exopolysaccharide export protein |
| RA | 1,065,700 | C→T | R415C (CGT→TGT) | yccE → | hypothetical protein |
| RA | 1,067,795 | A→G | S112S (AGT→AGC) | wrbA ← | predicted flavoprotein in Trp regulation |
| RA | 1,072,535 | (G)5→6 | coding (47/387 nt) | ycdK ← | hypothetical protein |
| RA | 1,091,749 | C→T | S321S (TCG→TCA) | ycdS ← | predicted outer membrane protein |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,132,556 | 2 bp→CA | intergenic (‑116/‑38) | flgA ← / → flgB | assembly protein for flagellar basal‑body periplasmic P ring/flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,132,560 | 1 bp→TT | intergenic (‑120/‑35) | flgA ← / → flgB | assembly protein for flagellar basal‑body periplasmic P ring/flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,139,752 | (G)5→6 | coding (805/942 nt) | flgJ → | muramidase |
| RA | 1,153,927 | A→G | T138A (ACG→GCG) | fabF → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II |
| RA | 1,194,589 | A→G | G254G (GGT→GGC) | trmU ← | tRNA (5‑methylaminomethyl‑2‑thiouridylate)‑ methyltransferase |
| RA | 1,256,829 | A→G | V234A (GTT→GCT) | ycgV ← | predicted adhesin |
| RA | 1,292,378 | T→C | V187A (GTG→GCG) | rssB → | response regulator of RpoS |
| RA | 1,303,712 | A→G | S273G (AGC→GGC) | oppA → | oligopeptide transporter subunit |
| RA | 1,341,506 | A→G | T155A (ACG→GCG) | pgpB → | phosphatidylglycerophosphate phosphatase B |
| RA | 1,369,160 | A→G | V156A (GTC→GCC) | pspF ← | DNA‑binding transcriptional activator |
| RA | 1,411,407 | G→A | L61L (TTG→TTA) | dbpA → | ATP‑dependent RNA helicase specific for 23S rRNA |
| MC JC | 1,413,639 | Δ23,060 bp | [ydaO]–ynaE | 30 genes [ydaO], intR, ydaQ, ydaC, lar, recT, recE, racC, ydaE, kil, sieB, ydaF, ydaG, racR, ydaS, ydaT, ydaU, ydaV, ydaW, rzpR, rzoR, trkG, ynaK, ydaY, ynaA, insH, stfR, tfaR, pinR, ynaE |
|
| RA | 1,464,573 | Δ1 bp | coding (735/1314 nt) | paaK → | phenylacetyl‑CoA ligase |
| RA | 1,609,104 | A→G | E15E (GAA→GAG) | tam → | trans‑aconitate methyltransferase |
| RA | 1,620,262 | Δ1 bp | coding (361/666 nt) | marC ← | predicted transporter |
| RA | 1,644,094 | T→C | intergenic (+313/+109) | cspF → / ← ydfT | cold shock protein/predicted antitermination protein Q |
| RA | 1,676,369 | (C)6→7 | coding (743/1035 nt) | ydgG → | predicted inner membrane protein |
| RA | 1,873,445 | C→T | T449T (ACC→ACT) | yeaI → | predicted diguanylate cyclase |
| RA | 1,955,601 | T→C | V149A (GTG→GCG) | yecP → | predicted methyltransferase |
| RA | 2,153,956 | T→C | E218E (GAA→GAG) | yegK ← | hypothetical protein |
| RA | 2,248,614 | G→A | A497V (GCA→GTA) | cirA ← | ferric iron‑catecholate outer membrane transporter |
| RA | 2,265,849 | T→C | K327K (AAA→AAG) | fruB ← | fused fructose‑specific PTS enzyme IIA component and HPr component |
| MC JC | 2,320,795 | Δ1,336 bp | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,356,229 | G→A | I272I (ATC→ATT) | glpT ← | sn‑glycerol‑3‑phosphate transporter |
| RA | 2,364,097 | T→C | Q242Q (CAA→CAG) | yfaV ← | predicted transporter |
| RA | 2,528,475 | G→A | G319G (GGC→GGT) | xapB ← | xanthosine transporter |
| RA | 2,532,671 | G→A | V94I (GTC→ATC) | yfeH → | predicted inner membrane protein |
| RA | 2,569,516 | T→C | T298A (ACC→GCC) | eutE ← | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| RA | 2,587,316 | T→C | Y356H (TAT→CAT) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,634,430 | T→C | Q14R (CAG→CGG) | yfgJ ← | hypothetical protein |
| RA | 2,651,283 | G→A | G45E (GGA→GAA) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,684,480 | (A)7→8 | intergenic (‑317/‑11) | glyA ← / → hmp | serine hydroxymethyltransferase/fused nitric oxide dioxygenase and dihydropteridine reductase 2 |
| RA | 2,705,226 | G→A | G185G (GGC→GGT) | lepA ← | GTP binding membrane protein |
| RA | 2,804,247 | T→C | D259D (GAT→GAC) | proV → | glycine betaine transporter subunit |
| RA | 2,857,875 | G→A | W709* (TGG→TGA) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,868,301 | C→T | P210P (CCG→CCA) | surE ← | broad specificity 5'(3')‑nucleotidase and polyphosphatase |
| RA | 2,886,049 | G→A | intergenic (‑174/+185) | ygcB ← / ← cysH | conserved hypothetical protein, member of DEAD box family/3'‑phosphoadenosine 5'‑phosphosulfate reductase |
| RA | 2,891,667 | T→C | C119R (TGC→CGC) | ygcN → | predicted oxidoreductase, FAD/NAD(P)‑binding domain |
| RA | 2,906,975 | C→G | D450H (GAC→CAC) | pyrG ← | CTP synthetase |
| RA | 2,919,665 | G→A | G364G (GGC→GGT) | gudP ← | predicted D‑glucarate transporter |
| RA | 2,937,297 | G→A | A402T (GCC→ACC) | fucK → | L‑fuculokinase |
| RA | 2,949,857 | G→A | L421L (CTG→TTG) | recD ← | exonuclease V (RecBCD complex), alpha chain |
| RA | 3,100,536 | A→G | V85A (GTG→GCG) | yggL ← | hypothetical protein |
| RA | 3,123,098 | A→G | C340R (TGC→CGC) | glcF ← | glycolate oxidase iron‑sulfur subunit |
| RA | 3,127,881 | G→A | R331C (CGC→TGC) | yghO ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,153,326 | G→A | I183I (ATC→ATT) | yqhC ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,169,789 | G→A | R217Q (CGG→CAG) | qseC → | sensory histidine kinase in two‑component regulatory system with QseB |
| RA | 3,215,778 | T→C | I115T (ATC→ACC) | yqjI → | predicted transcriptional regulator |
| RA | 3,222,265 | T→C | L326P (CTG→CCG) | ebgA → | cryptic beta‑D‑galactosidase, alpha subunit |
| RA | 3,247,179 | T→C | S29P (TCC→CCC) | yqjB → | hypothetical protein |
| MC JC | 3,261,134 | Δ1,199 bp | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,266,304 | T→C | Y206C (TAC→TGC) | tdcA ← | DNA‑binding transcriptional activator |
| RA | 3,402,600 | G→A | S196S (AGC→AGT) | yhdA ← | conserved inner membrane protein |
| RA | 3,405,975 | C→T | S68S (AGC→AGT) | accC → | acetyl‑CoA carboxylase, biotin carboxylase subunit |
| RA | 3,557,661 | A→G | intergenic (‑271/+582) | yiiE ← / ← yiiD | predicted transcriptional regulator/predicted acetyltransferase |
| RA | 3,624,613 | T→C | L250P (CTG→CCG) | metR → | DNA‑binding transcriptional activator, homocysteine‑binding |
| RA | 3,636,914 | T→C | E595E (GAA→GAG) | uvrD ← | DNA‑dependent ATPase I and helicase II |
| RA | 3,656,842 | G→A | I413I (ATC→ATT) | wzyE ← | predicted Wzy protein involved in ECA polysaccharide chain elongation |
| RA | 3,711,417 | G→A | A124T (GCG→ACG) | gidA → | glucose‑inhibited cell‑division protein |
| RA | 3,725,678 | G→A | A175T (GCG→ACG) | pstS → | phosphate transporter subunit |
| MC JC | 3,742,936 | Δ1,336 bp | insD–insC | insD, insC | |
| RA | 3,912,304 | (G)8→10 | coding (1261/1455 nt) | xylB → | xylulokinase |
| RA | 4,017,654 | C→T | R1190R (CGG→CGA) | rhsB ← | rhsB element core protein RshB |
| RA | 4,051,195 | C→T | R270C (CGT→TGT) | ugpE → | glycerol‑3‑phosphate transporter subunit |
| RA | 4,144,590 | A→G | F606L (TTT→CTT) | nirB ← | nitrite reductase, large subunit, NAD(P)H‑binding |
| RA | 4,245,382 | C→T | A155T (GCT→ACT) | xylE ← | D‑xylose transporter |
| RA | 4,278,307 | C→T | intergenic (+56/+43) | ssb → / ← yjcB | Single‑stranded DNA‑binding protein/predicted inner membrane protein |
| RA | 4,343,161 | A→G | V681A (GTA→GCA) | adiA ← | biodegradative arginine decarboxylase |
| RA | 4,344,956 | G→A | R83C (CGC→TGC) | adiA ← | biodegradative arginine decarboxylase |
| RA | 4,357,741 | A→G | L52L (TTA→TTG) | yjdO → | hypothetical protein |
| RA | 4,371,274 | (A)5→3 | intergenic (‑9/+296) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,381,155 | C→T | intergenic (+33/‑78) | ecnA → / → ecnB | entericidin A membrane lipoprotein, antidote entericidin B/entericidin B membrane lipoprotein |
| RA | 4,444,533 | C→T | intergenic (+60/+19) | ytfK → / ← ytfL | hypothetical protein/predicted inner membrane protein |
| RA | 4,558,099 | T→C | R173R (CGT→CGC) | uxuB → | D‑mannonate oxidoreductase, NAD‑binding |
| RA | 4,585,134 | (A)7→8 | coding (1009/1395 nt) | hsdS ← | specificity determinant for hsdM and hsdR |
| RA | 4,642,006 | G→A | A211T (GCC→ACC) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB, regulator of the CreBC regulon |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | AC_000091 | 1301041–1302370 | 1302407 | 38–1367 | 152 [0] | [0] 114 | insC–insD | insC,insD |
| * | * | ÷ | AC_000091 | 1397797–1398957 | 1401959 | 3003–4163 | 69 [66] | [0] 170 | [insH]–ogt | [insH],ynaJ,uspE,fnr,ogt |
| * | * | ÷ | AC_000091 | 3690506–3690766 | 3693239–3692694 | 1929–2734 | 70 [68] | [67] 72 | [rrlC]–[gltU] | [rrlC],[gltU] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | AC_000091 | 1209367 = | 21 (0.160) | 86 (0.790) | 65/146 | 0.7 | 83.4% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | AC_000091 | 1211196 = | 17 (0.160) | intergenic (‑500/‑66) | tfaE/pin | predicted tail fiber assembly protein/site‑specific DNA recombinase | |||||
| * | ? | AC_000091 | = 1209382 | 21 (0.160) | 59 (0.540) | 49/146 | 2.3 | 77.5% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | AC_000091 | = 1211179 | 17 (0.160) | intergenic (‑483/‑83) | tfaE/pin | predicted tail fiber assembly protein/site‑specific DNA recombinase | |||||
| * | ? | AC_000091 | = 1301040 | 0 (0.000) | 99 (1.090) +28 bp |
68/122 | 0.1 | 100% | intergenic (+218/‑90) | ychE/insC | predicted inner membrane protein/IS2 element protein |
| ? | AC_000091 | = 4311564 | NA (NA) | coding (914/1029 nt) | alsK | D‑allose kinase | |||||
| * | ? | AC_000091 | 1302408 = | 0 (0.000) | 112 (0.840) | 75/178 | 1.0 | 100% | intergenic (+50/‑488) | insD/oppA | IS2 element protein/oligopeptide transporter subunit |
| ? | AC_000091 | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/insH | conserved inner membrane protein/IS5 transposase and trans‑activator | |||||
| * | ? | AC_000091 | = 1398951 | NA (NA) | 155 (1.170) | 80/176 | 0.7 | 100% | intergenic (+145/‑128) | insH/ynaJ | IS5 transposase and trans‑activator/predicted inner membrane protein |
| ? | AC_000091 | 1401960 = | 0 (0.000) | intergenic (‑10/+1) | ogt/abgT | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase/predicted cryptic aminobenzoyl‑glutamate transporter | |||||
| * | ? | AC_000091 | = 2176982 | 0 (0.000) | 119 (0.940) | 82/168 | 0.4 | 100% | coding (71/321 nt) | gatA | galactitol‑specific enzyme IIA component of PTS |
| ? | AC_000091 | 2178182 = | 0 (0.000) | coding (202/315 nt) | gatA | galactitol‑specific enzyme IIA component of PTS | |||||
| * | ? | AC_000091 | = 3746910 | 0 (0.000) | 117 (0.920) | 86/170 | 0.3 | 100% | coding (71/447 nt) | tnaB | tryptophan transporter of low affinity |
| ? | AC_000091 | 3748110 = | 0 (0.000) | coding (871/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | AC_000091 | 3748316 = | 12 (0.090) | 163 (1.220) | 108/178 | 0.0 | 93.1% | coding (665/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | AC_000091 | = 4056987 | NA (NA) | coding (388/414 nt) | yrhA | hypothetical protein | |||||
| * | ? | AC_000091 | = 3748324 | 18 (0.130) | 142 (1.060) | 99/178 | 0.1 | 88.8% | coding (657/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | AC_000091 | 4056220 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | AC_000091 | = 3750590 | 0 (0.000) | 162 (1.270) | 93/170 | 0.1 | 100% | intergenic (‑104/‑69) | tnaA/insH | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/IS5 element protein |
| ? | AC_000091 | 3751790 = | 0 (0.000) | intergenic (+151/+116) | insH/tnaC | IS5 element protein/tryptophanase leader peptide | |||||
| * | ? | AC_000091 | 4056221 = | NA (NA) | 155 (1.170) | 99/176 | 0.1 | 92.3% | intergenic (‑565/+14) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' |
| ? | AC_000091 | 4370787 = | 13 (0.100) | coding (479/1116 nt) | dcuA | C4‑dicarboxylate antiporter | |||||
| * | ? | AC_000091 | = 4056987 | NA (NA) | 125 (0.930) | 88/178 | 0.3 | 89.3% | coding (388/414 nt) | yrhA | hypothetical protein |
| ? | AC_000091 | = 4370795 | 15 (0.110) | coding (471/1116 nt) | dcuA | C4‑dicarboxylate antiporter | |||||
| * | ? | AC_000091 | = 4310362 | 0 (0.000) | 129 (1.010) | 85/170 | 0.3 | 98.9% | intergenic (‑286/‑69) | yjcS/insH | predicted alkyl sulfatase/IS5 element protein |
| ? | AC_000091 | 4311562 = | 3 (0.020) | coding (916/1029 nt) | alsK | D‑allose kinase | |||||