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 | 42,108 | G→A | intergenic (‑177/‑295) | caiT ← / → fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| RA | 122,761 | C→T | H224Y (CAT→TAT) | pdhR → | DNA‑binding transcriptional dual regulator PdhR |
| RA | 229,552 | C→T | S129F (TCC→TTC) | dkgB → | methylglyoxal reductase DkgB |
| RA | 243,409 | C→A | intergenic (‑106/‑134) | fadE ← / → gmhA | acyl‑CoA dehydrogenase/D‑sedoheptulose 7‑phosphate isomerase |
| 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 |
| MC JC | 377,430 | Δ100 bp | intergenic (+119/+6) | yaiL → / ← frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| JC JC | 480,896 | IS5 (+) +4 bp | intergenic (‑188/+355) | tomB ← / ← acrB | Hha toxicity modulator TomB/multidrug efflux pump RND permease AcrB |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 790,832 | Δ1 bp | coding (198/1047 nt) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| JC JC | 791,653 | IS1 (–) +8 bp | coding (396‑403/1017 nt) | galE ← | UDP‑glucose 4‑epimerase |
| RA | 1,001,251 | A→C | Q679P (CAA→CCA) | elfC → | putative fimbrial usher protein ElfC |
| JC JC | 1,034,134 | IS30 (–) +2 bp | coding (881‑882/1794 nt) | hyaB → | hydrogenase 1 large subunit |
| RA | 1,103,599 | G→T | intergenic (‑403/‑352) | csgD ← / → csgB | DNA‑binding transcriptional dual regulator CsgD/curlin, minor subunit |
| 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 | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,196,316 | T→A | D398E (GAT→GAA) | icd → | isocitrate dehydrogenase |
| JC | 1,287,262 | +68 bp | noncoding (67/85 nt) | tyrV ← | tRNA‑Tyr |
| RA | 1,287,294 | C→G | noncoding (35/85 nt) | tyrV ← | tRNA‑Tyr |
| JC JC | 1,293,326 | IS1 (–) +9 bp | intergenic (‑404/‑193) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,302,204 | Δ1 bp | coding (1023/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,302,207 | +A | coding (1026/1632 nt) | 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 | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,371,391 | C→T | S392S (AGC→AGT) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,407,078 | T→A | T240S (ACT→TCT) | dgcM ← | diguanylate cyclase DgcM |
| JC JC | 1,434,661 | IS2 (–) +5 bp | intergenic (‑255/+520) | ynaM ← / ← uspF | protein YnaM/universal stress protein F |
| JC JC | 1,545,555 | IS5 (–) +4 bp | coding (157‑160/957 nt) | yddK ← | leucine‑rich repeat domain‑containing protein YddK |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| JC JC | 1,647,146 | IS3 (+) +3 bp | intergenic (+409/+26) | flxA → / ← ydfW | PF14282 family protein FlxA/protein YdfW |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,757,463 | T→C | S15P (TCT→CCT) | lpp → | murein lipoprotein |
| 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 |
| RA | 1,948,964 | G→A | A520V (GCT→GTT) | aspS ← | aspartate‑‑tRNA ligase |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA5 ← / → uspC | IS1 family protein InsA/universal stress protein C |
| RA | 2,003,198 | C→A | V137L (GTG→TTG) | fliC ← | flagellar filament structural protein |
| 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 | 2,238,689 | IS1 (+) +8 bp | coding (594‑601/1521 nt) | mglA ← | D‑galactose/methyl‑galactoside ABC transporter ATP binding subunit |
| JC JC | 2,375,828 | IS186 (+) +4 bp | coding (132‑135/963 nt) | menC ← | o‑succinylbenzoate synthase |
| RA | 2,413,411 | C→T | intergenic (‑279/‑59) | yfbV ← / → ackA | PF04217 family membrane protein YfbV/acetate kinase |
| RA | 2,414,829 | A→G | E28G (GAA→GGA) | pta → | phosphate acetyltransferase |
| JC JC | 2,415,251 | IS30 (–) +2 bp | coding (505‑506/2145 nt) | pta → | phosphate acetyltransferase |
| 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 | 2,599,947 | G→T | L14F (TTG→TTT) | gcvR → | putative transcriptional regulator GcvR |
| RA | 2,612,191 | G→T | G98* (GGA→TGA) | hyfR → | DNA‑binding transcriptional activator HyfR |
| 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 | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| 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 | 3,388,041 | 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 | 3,689,145 | G→T | T10K (ACG→AAG) | bcsC ← | cellulose synthase outer membrane channel |
| RA | 3,696,157 | G→T | P10H (CCT→CAT) | yhjR ← | PF10945 family protein YhjR |
| RA | 3,703,531 | G→T | Y106* (TAC→TAA) | dppD ← | dipeptide ABC transporter ATP binding subunit DppD |
| 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 | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,828,778 | C→A | intergenic (‑113/‑167) | gltS ← / → xanP | glutamate:sodium symporter/xanthine:H(+) symporter XanP |
| JC JC | 4,123,967 | IS3 (–) +4 bp | coding (487‑490/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,128,813 | Δ2 bp | coding (142‑143/1161 nt) | metB → | O‑succinylhomoserine(thiol)‑lyase/O‑ succinylhomoserine lyase |
| RA | 4,171,438 | Δ2 bp | noncoding (2798‑2799/2904 nt) | rrlB → | 23S ribosomal RNA |
| RA | 4,171,788 | G→T | intergenic (+32/‑269) | rrfB → / → murB | 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,359,314 | G→A | Q240* (CAG→TAG) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,380,292 | 2 bp→A | coding (225‑226/735 nt) | frdB ← | fumarate reductase iron‑sulfur protein |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,436,956 | 2 bp→TT | coding (202‑203/741 nt) | cysQ → | 3'(2'),5'‑bisphosphate nucleotidase |
| JC JC | 4,440,451 | IS2 (–) +5 bp | coding (761‑765/1344 nt) | paeA ← | putative cadaverine/putrescine exporter |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| 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 |
| MC JC | 4,628,621 | Δ6,226 bp | ettA–[rob] | ettA, slt, trpR, yjjX, ytjC, [rob] | |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 323451 | 362203 | 38753 | 84 [0] | [0] 94 | [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 | 1196325 | 1211412 | 15088 | 19 [17] | [0] 19 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1907645 | 1907878 | 234 | 84 [0] | [0] 102 | yobF/yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| * | * | ÷ | NC_000913 | 2553281 | 2555914 | 2634 | 18 [16] | [16] 18 | [hemF]–[eutL] | [hemF],eutR,eutK,[eutL] |
| * | * | ÷ | NC_000913 | 3423900–3424233 | 3424412–3424238 | 6–513 | 18 [17] | [15] 18 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4166899–4168219 | 4168497 | 279–1599 | 18 [17] | [13] 19 | [rrsB]–gltT | [rrsB],gltT |
| * | * | ÷ | NC_000913 | 4287379 | 4310371 | 22993 | 113 [0] | [0] 129 | ytcB–[alsA] | ytcB,nrfA,nrfB,nrfC,nrfD,nrfE,nrfF,nrfG,gltP,yjcO,fdhF,mdtP,mdtO,mdtN,ytcA,yjcS,alsK,alsE,alsC,[alsA] |
| * | * | ÷ | NC_000913 | 4542159 | 4592305 | 50147 | 120 [0] | [0] 52 | [fimE]–[tsr] | [fimE],fimA,fimI,fimC,fimD,fimF,fimG,fimH,gntP,uxuA,uxuB,uxuR,yjiC,ytiC,ytiD,idlP,iraD,hypT,iadA,yjiG,yjiH,kptA,yjiJ,yjiK,ytiA,yjiL,yjiM,yjiN,mdtM,ytiE,yjiR,yjiS,yjiT,mcrC,mcrB,mcrB,symE,symR,hsdS,hsdM,hsdR,mrr,yjiA,yjiX,btsT,[tsr] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 138 (1.500) | 73/582 | 0.1 | 100% | 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) | 84 (0.890) | 66/598 | 0.2 | 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) | 92 (0.970) | 70/598 | 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 | = 1299498 | 1 (0.010) | 114 (1.220) | 68/590 | 0.1 | 99.6% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1907644 | 0 (0.000) | 84 (0.890) | 60/598 | 0.3 | 100% | intergenic (‑53/+617) | yobF/yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1907879 = | 0 (0.000) | 102 (1.080) | 66/598 | 0.2 | 100% | intergenic (‑288/+382) | yobF/yebO | DUF2527 domain‑containing protein YobF/uncharacterized protein YebO |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1978502 | 4 (0.040) | 95 (1.030) | 54/582 | 0.4 | 98.0% | 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 | 3583428 = | NA (NA) | 128 (1.350) | 86/598 | 0.0 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4310372 = | 0 (0.000) | coding (609/1533 nt) | alsA | D‑allose ABC transporter ATP binding subunit | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 121 (1.280) | 88/598 | 0.0 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542158 | 0 (0.000) | coding (122/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 112 (1.180) | 74/598 | 0.1 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4287378 | 0 (0.000) | intergenic (‑7/‑233) | acs/ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 52 (0.550) | 39/598 | 0.9 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4592306 = | 0 (0.000) | coding (650/1656 nt) | tsr | methyl‑accepting chemotaxis protein Tsr | |||||