mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 3,645 | G→A | W282* (TGG→TAG) | thrB → | homoserine kinase |
| RA | 13,947 | C→T | S595S (TCC→TCT) | dnaK → | chaperone protein DnaK |
| RA | 53,713 | C→T | Q330Q (CAG→CAA) | surA ← | chaperone SurA |
| RA | 56,144 | A→G | D322D (GAT→GAC) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 57,768 | C→T | I135I (ATC→ATT) | djlA → | co‑chaperone protein DjlA |
| RA | 81,102 | G→A | S286L (TCG→TTG) | leuB ← | 3‑isopropylmalate dehydrogenase |
| RA | 124,499 | A→C | T495P (ACC→CCC) | aceE → | pyruvate dehydrogenase E1 component |
| RA | 134,058 | C→T | A815V (GCG→GTG) | acnB → | AcnB |
| RA | 134,922 | C→T | E221K (GAG→AAG) | speD ← | S‑adenosylmethionine decarboxylase proenzyme |
| RA | 156,068 | A→G | V45A (GTA→GCA) | yadV ← | putative fimbrial chaperone YadV |
| RA | 156,591 | T→C | K98R (AAA→AGA) | yadN ← | putative fimbrial protein YadN |
| RA | 167,798 | C→A | Y105* (TAC→TAA) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 196,033 | G→T | L119F (TTG→TTT) | cdsA → | CDP‑diglyceride synthetase |
| RA | 225,750 | G→A | intergenic (+175/‑9) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 229,552 | C→T | S129F (TCC→TTC) | dkgB → | methylglyoxal reductase DkgB |
| JC JC | 258,921 | IS1 (+) +9 bp | pseudogene (246‑254/331 nt) | crl → | RNA polymerase holoenzyme assembly factor Crl |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 363,282 | G→T | F1008L (TTC→TTA) | lacZ ← | beta‑galactosidase |
| RA | 365,307 | G→A | F333F (TTC→TTT) | lacZ ← | beta‑galactosidase |
| JC JC | 366,068 | IS1 (+) +8 bp | coding (231‑238/3075 nt) | lacZ ← | beta‑galactosidase |
| MC JC | 680,166 | Δ7,685 bp | IS5‑mediated | [ybeU]–gltI | [ybeU], djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 835,360 | C→T | P38L (CCT→CTT) | ybiB → | nonspecific DNA‑binding protein YbiB |
| RA | 1,001,251 | A→C | Q679P (CAA→CCA) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,148,972 | C→T | Q72* (CAG→TAG) | fabH → | 3‑oxoacyl‑[acyl carrier protein] synthase 3 |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,287,040 | G→A | intergenic (+56/+26) | ychS → / ← rttR | putative uncharacterized protein YchS/small RNA RttR |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,336,674 | G→A | G282R (GGG→AGG) | acnA → | aconitate hydratase 1 |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,339,315 | C→T | intergenic (‑155/‑15) | ribA ← / → pgpB | GTP cyclohydrolase 2/phosphatidylglycerophosphatase B |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,448,427 | G→A | G303G (GGG→GGA) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,556,428 | G→A | intergenic (‑148/‑197) | bdm ← / → osmC | biofilm‑dependent modulation protein/osmotically inducible peroxiredoxin OsmC |
| RA | 1,600,491 | C→A | A251S (GCA→TCA) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,733,241 | IS30 (+) +2 bp | coding (4155‑4156/4617 nt) | lhr → | ATP‑dependent helicase Lhr |
| RA | 1,756,250 | G→A | G185S (GGC→AGC) | pykF → | pyruvate kinase 1 |
| RA | 1,829,887 | G→A | A293A (GCC→GCT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,979,518 | IS5 (+) +4 bp | intergenic (‑303/‑232) | insA5 ← / → uspC | IS1 family protein InsA/universal stress protein C |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,042,171 | G→A | intergenic (+146/‑197) | zinT → / → yodB | metal‑binding protein ZinT/putative cytochrome b561 YodB |
| RA | 2,044,642 | T→C | intergenic (+18/‑296) | asnT → / → yeeJ | tRNA‑Asn/inverse autotransporter adhesin |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,173,448 | C→T | intergenic (‑575/+834) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,177,243 | IS1 (–) +9 bp | intergenic (‑39/+261) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2/fructose‑bisphosphate aldolase class I |
| JC JC | 2,468,298 | IS3 (+) +3 bp | coding (85‑87/921 nt) | yfdH → | bactoprenol glucosyl transferase |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 3,152,494 | G→T | A87S (GCG→TCG) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase |
| RA | 3,160,073 | C→T | K358K (AAG→AAA) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| JC JC | 3,267,967 | IS1 (+) +8 bp | coding (114‑121/540 nt) | yhaB → | protein YhaB |
| RA | 3,293,086 | C→T | G84R (GGG→AGG) | rsmI ← | 16S rRNA 2'‑O‑ribose C1402 methyltransferase |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| JC JC | 3,350,556 | IS1 (–) +8 bp | intergenic (‑97/‑14) | elbB ← / → arcZ | low activity glyoxalase ElbB/small regulatory RNA ArcZ |
| RA | 3,355,505 | C→T | P261S (CCG→TCG) | gltB → | glutamate synthase subunit GltB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,429,986 | IS3 (–) +5 bp :: +T | coding (34‑38/258 nt) | yrdB ← | DUF1488 domain‑containing protein YrdB |
| RA | 3,560,443 | C→G | intergenic (+577/+179) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,666,149 | C→T | intergenic (‑339/+31) | gadX ← / ← gadA | DNA‑binding transcriptional dual regulator GadX/glutamate decarboxylase A |
| RA | 3,676,409 | C→T | A648T (GCT→ACT) | yhjG ← | AsmA family protein YhjG |
| RA | 3,677,529 | C→T | M274I (ATG→ATA) | yhjG ← | AsmA family protein YhjG |
| RA | 3,677,614 | C→T | G246E (GGG→GAG) | yhjG ← | AsmA family protein YhjG |
| RA | 3,707,883 | G→A | intergenic (‑178/+733) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,756,684 | C→T | A382T (GCG→ACG) | yiaY ← | L‑threonine dehydrogenase |
| RA | 3,757,425 | C→T | A135T (GCC→ACC) | yiaY ← | L‑threonine dehydrogenase |
| RA | 3,760,854 | C→T | R132R (CGG→CGA) | selA ← | selenocysteine synthase |
| RA | 3,773,180 | C→T | I300I (ATC→ATT) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,781,190 | C→T | intergenic (+173/‑25) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,786,535 | G→A | E426K (GAA→AAA) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,786,612 | G→A | M451I (ATG→ATA) | gpmM → | 2,3‑bisphosphoglycerate‑independent phosphoglycerate mutase |
| RA | 3,787,021 | G→A | A62T (GCA→ACA) | envC → | murein hydrolase activator EnvC |
| RA | 3,804,350 | C→T | G256D (GGT→GAT) | waaS ← | lipopolysaccharide core biosynthesis protein WaaS |
| RA | 3,809,362 | C→T | P275S (CCG→TCG) | waaA → | KDO transferase |
| RA | 3,814,306 | A→G | V126V (GTA→GTG) | dut → | dUTP diphosphatase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,822,274 | G→A | G57S (GGT→AGT) | rpoZ → | RNA polymerase subunit omega |
| RA | 3,829,931 | C→T | F329F (TTC→TTT) | xanP → | xanthine:H(+) symporter XanP |
| RA | 3,872,926 | C→T | G25S (GGC→AGC) | dgoD ← | D‑galactonate dehydratase |
| RA | 3,897,929 | C→T | P142S (CCC→TCC) | cbrB → | putative inner membrane protein |
| RA | 3,900,536 | G→A | S14S (AGC→AGT) | yieL ← | putative hydrolase YieL |
| RA | 3,905,813 | C→T | G252D (GGT→GAT) | bglG ← | transcriptional antiterminator BglG |
| RA | 3,918,717 | C→T | A381T (GCA→ACA) | atpA ← | ATP synthase F1 complex subunit alpha |
| RA | 3,928,064 | C→T | L304L (CTG→TTG) | asnA → | asparagine synthetase A |
| RA | 3,929,487 | G→A | F39F (TTC→TTT) | viaA ← | protein ViaA |
| RA | 3,930,350 | G→A | V248V (GTC→GTT) | ravA ← | regulatory ATPase RavA |
| RA | 4,117,408 | C→T | R228K (AGA→AAA) | glpF ← | glycerol facilitator |
| RA | 4,119,000 | C→T | A111T (GCG→ACG) | rraA ← | ribonuclease E inhibitor protein A |
| RA | 4,119,288 | C→T | D15N (GAT→AAT) | rraA ← | ribonuclease E inhibitor protein A |
| RA | 4,138,814 | G→A | D74D (GAC→GAT) | gldA ← | L‑1,2‑propanediol dehydrogenase/glycerol dehydrogenase |
| RA | 4,144,951 | C→T | F319F (TTC→TTT) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,145,392 | C→T | R466R (CGC→CGT) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,146,248 | G→A | E752K (GAG→AAG) | pflD → | putative formate acetyltransferase 2 |
| RA | 4,156,917 | T→C | L23P (CTG→CCG) | argH → | argininosuccinate lyase |
| RA | 4,159,997 | A→T | L265Q (CTG→CAG) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,160,765 | G→A | A9V (GCC→GTC) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,175,817 | C→T | noncoding (64/76 nt) | thrT → | tRNA‑Thr |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,212,959 | G→C | intergenic (+13/‑81) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 4,212,973 | Δ1 bp | intergenic (+27/‑67) | rrlE → / → rrfE | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,287,464 | T→A | intergenic (‑93/‑147) | acs ← / → ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB |
| RA | 4,294,266 | T→C | intergenic (+127/‑215) | nrfG → / → gltP | putative formate‑dependent nitrite reductase complex subunit NrfG/glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,326,428 | G→A | L103L (CTG→TTG) | yjdM ← | zinc ribbon domain‑containing protein YjdM |
| RA | 4,355,470 | A→G | N314N (AAT→AAC) | dtpC ← | dipeptide/tripeptide:H(+) symporter DtpC |
| RA | 4,427,149 | C→T | A92T (GCT→ACT) | yjfZ ← | DUF2686 domain‑containing protein YjfZ |
| RA | 4,427,694 | C→T | intergenic (‑272/+385) | yjfZ ← / ← ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| RA | 4,447,516 | C→T | D1135D (GAC→GAT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,483,872 | C→T | A137T (GCT→ACT) | holC ← | DNA polymerase III subunit chi |
| RA | 4,494,833 | C→T | L71F (CTT→TTT) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,496,519 | C→T | intergenic (+30/‑1753) | leuX → / → insC6 | tRNA‑Leu/IS2 insertion element repressor InsA |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| JC JC | 4,542,042 | IS1 (+) +8 bp | coding (6‑13/597 nt) | fimE → | regulator for fimA |
| RA | 4,542,295 | A→G | T87A (ACC→GCC) | fimE → | regulator for fimA |
| RA | 4,563,778 | (G)6→5 | coding (148/258 nt) | ytiA ← | uncharacterized protein YtiA |
| RA | 4,585,480 | G→A | Q428* (CAA→TAA) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,602,509 | C→T | W117* (TGG→TAG) | yjjP ← | putative succinate exporter YjjP |
| RA | 4,616,669 | G→T | L133I (CTA→ATA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| RA | 4,632,081 | C→T | A450V (GCT→GTT) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 323451 | 362203 | 38753 | 71 [0] | [0] 110 | [ykgF]–[lacY] | [ykgF],ykgG,ykgH,betA,betB,betI,betT,yahV,pdeL,yahB,yahC,yahD,yahE,yahF,yahG,yahH,yahI,yahJ,yahK,yahL,yahM,yahN,yahO,prpR,prpB,prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,cynX,lacA,[lacY] |
| * | * | ÷ | NC_000913 | 3423733–3424232 | 3424486–3424238 | 7–754 | 29 [27] | [26] 29 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 11 (0.130) | 97 (1.160) | 57/572 | 0.2 | 94.8% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 71 (0.830) | 47/588 | 0.5 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 323450 | 0 (0.000) | coding (1113/1428 nt) | ykgF | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 110 (1.280) | 69/588 | 0.1 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 0 (0.000) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | 1207790 = | 23 (0.270) | 65 (0.800) | 45/556 | 0.5 | 66.4% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 44 (0.540) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.290) | 41 (0.500) | 31/556 | 1.3 | 54.8% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 44 (0.540) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1978502 | 51 (0.590) | 99 (1.180) | 56/572 | 0.2 | 80.0% | intergenic (‑305/+16) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA5/uspC | IS1 family protein InsA/universal stress protein C | |||||
| * | ? | NC_000913 | 4542682 = | 72 (0.840) | 35 (0.420) | 26/570 | 1.9 | 32.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 74 (0.890) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 84 (0.980) | 42 (0.500) | 39/570 | 0.8 | 35.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 74 (0.890) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||