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 | 81,102 | G→A | S286L (TCG→TTG) | leuB ← | 3‑isopropylmalate dehydrogenase |
| 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 | 229,552 | C→T | S129F (TCC→TTC) | dkgB → | methylglyoxal reductase DkgB |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| 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 | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 1,001,251 | A→C | Q679P (CAA→CCA) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,125,694 | Δ1 bp | coding (133/585 nt) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| 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 |
| JC JC | 1,293,212 | IS1 (+) +8 bp | intergenic (‑290/‑308) | 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 |
| JC JC | 1,302,156 | IS1 (+) +8 bp | coding (975‑982/1632 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 | 1,336,674 | 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 | 1,643,679 | 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 | 1,656,657 | IS1 (–) +9 bp | coding (474‑482/561 nt) | speG → | spermidine N‑acetyltransferase |
| JC JC | 1,744,583 | IS1 (+) +8 bp | coding (1127‑1134/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| 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 | 2,025,277 | C→A | noncoding (37/91 nt) | dsrA ← | small regulatory RNA DsrA |
| 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 | 2,176,491 | IS1 (+) +9 bp | coding (706‑714/855 nt) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 |
| RA | 2,259,415 | +G | intergenic (‑119/+304) | psuK ← / ← fruA | putative pseudouridine kinase/fructose‑specific PTS multiphosphoryl transfer protein FruA |
| JC | 2,406,557 | (TGCGGCAGC)1→2 | coding (85/939 nt) | lrhA ← | DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,415,865 | G→T | W373C (TGG→TGT) | pta → | phosphate acetyltransferase |
| JC JC | 2,468,298 | IS3 (+) +3 bp | coding (85‑87/921 nt) | yfdH → | bactoprenol glucosyl transferase |
| 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 | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| JC JC | 3,262,613 | IS1 (–) +9 bp | coding (1040‑1048/1209 nt) | tdcD ← | propionate kinase |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,202 | A→T | F309I (TTT→ATT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| JC JC | 3,429,986 | IS3 (–) +5 bp :: +T | coding (34‑38/258 nt) | yrdB ← | DUF1488 domain‑containing protein YrdB |
| RA | 3,444,896 | G→A | R112C (CGC→TGC) | rpsE ← | 30S ribosomal subunit protein S5 |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,551,406 | C→T | W356* (TGG→TGA) | malP ← | maltodextrin phosphorylase |
| 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 | 3,707,883 | 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 | 3,827,562 | G→T | H368Q (CAC→CAA) | gltS ← | glutamate:sodium symporter |
| RA | 3,828,776 | C→A | intergenic (‑111/‑169) | gltS ← / → xanP | glutamate:sodium symporter/xanthine:H(+) symporter XanP |
| RA | 3,918,297 | T→C | intergenic (‑32/+19) | atpG ← / ← atpA | ATP synthase F1 complex subunit gamma/ATP synthase F1 complex subunit alpha |
| JC JC | 4,117,984 | IS30 (+) +2 bp | coding (106‑107/846 nt) | glpF ← | glycerol facilitator |
| JC | 4,123,900 | Δ7 bp | coding (551‑557/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,182,361 | G→A | G373S (GGC→AGC) | rpoB → | RNA polymerase subunit beta |
| 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 | 4,296,381 | +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 | 4,473,900 | 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 | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,563,778 | (G)6→5 | coding (148/258 nt) | ytiA ← | uncharacterized protein YtiA |
| RA | 4,616,669 | G→T | L133I (CTA→ATA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 323451 | 325515 | 2065 | 32 [0] | [0] 2 | [ykgF]–ykgH | [ykgF],ykgG,ykgH |
| * | * | ÷ | NC_000913 | 325689 | 325996 | 308 | 3 [1] | [1] 2 | betA | choline dehydrogenase |
| * | * | ÷ | NC_000913 | 326248 | 327623 | 1376 | 2 [1] | [1] 2 | [betA]–[betB] | [betA],[betB] |
| * | * | ÷ | NC_000913 | 327933 | 334737 | 6805 | 2 [1] | [1] 2 | [betB]–[yahC] | [betB],betI,betT,yahV,pdeL,yahB,[yahC] |
| * | * | ÷ | NC_000913 | 334989 | 338900 | 3912 | 2 [1] | [1] 2 | [yahC]–[yahG] | [yahC],yahD,yahE,yahF,[yahG] |
| * | * | ÷ | NC_000913 | 339043 | 362203 | 23161 | 2 [1] | [0] 26 | [yahG]–[lacY] | [yahG],yahH,yahI,yahJ,yahK,yahL,yahM,yahN,yahO,prpR,prpB,prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,cynX,lacA,[lacY] |
| * | * | ÷ | NC_000913 | 679349 | 682981 | 3633 | 17 [0] | [1] 2 | [ybeT]–[hscC] | [ybeT],ybeU,djlC,[hscC] |
| * | * | ÷ | NC_000913 | 683126 | 685405 | 2280 | 2 [1] | [1] 2 | [hscC]–[gltK] | [hscC],rihA,gltL,[gltK] |
| * | * | ÷ | NC_000913 | 685656 | 686988 | 1333 | 2 [1] | [0] 2 | [gltK]–[gltI] | [gltK],gltJ,sroC,[gltI] |
| * | * | ÷ | NC_000913 | 687187 | 688849–687846 | 660–1663 | 2 [0] | [1] 2 | [gltI]–[insH3] | [gltI],[insH3] |
| * | * | ÷ | NC_000913 | 1979272 | 1979277 | 6 | 2 [1] | [0] 2 | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| * | * | ÷ | NC_000913 | 2558699 | 2563101 | 4403 | 39 [1] | [0] 2 | intZ–[yffP] | intZ,yffL,yffM,yffN,yffO,[yffP] |
| * | * | ÷ | NC_000913 | 2563286 | 2565488 | 2203 | 2 [0] | [0] 37 | yffQ–[eutA] | yffQ,yffR,yffS,[eutA] |
| * | * | ÷ | NC_000913 | 3423903–3424234 | 3424404–3424238 | 5–502 | 2 [1] | [1] 2 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035401–4036845 | 4036845 | 1–1445 | 2 [1] | [0] 2 | [rrsA] | [rrsA] |
| * | * | ÷ | NC_000913 | 4542050 | 4544011 | 1962 | 30 [0] | [0] 2 | [fimE]–[fimI] | [fimE],fimA,[fimI] |
| * | * | ÷ | NC_000913 | 4544361 | 4545798 | 1438 | 2 [1] | [0] 56 | [fimC]–[fimD] | [fimC],[fimD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 32 (0.750) | 31/492 | 0.3 | 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) | 26 (0.610) | 24/492 | 0.5 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 362204 = | 0 (0.000) | coding (976/1254 nt) | lacY | lactose permease | |||||
| * | ? | NC_000913 | = 679348 | 0 (0.000) | 17 (0.400) | 17/492 | 0.8 | 100% | coding (59/555 nt) | ybeT | Sel1 repeat‑containing protein YbeT |
| ? | NC_000913 | 687851 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.070) | 8 (0.200) | 7/460 | 1.6 | 73.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 3 (0.080) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 7 (0.170) | 7/484 | 1.6 | 100% | 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 | = 1978502 | 0 (0.000) | 11 (0.270) | 11/476 | 1.2 | 100% | 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 | 1978503 = | NA (NA) | 56 (1.320) | 52/492 | 0.1 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 4545799 = | 0 (0.000) | coding (704/2637 nt) | fimD | type I fimbriae usher protein | |||||
| * | ? | NC_000913 | = 2558698 | 1 (0.020) | 37 (0.900) | 35/476 | 0.2 | 98.7% | intergenic (‑19/‑160) | eutB/intZ | ethanolamine ammonia‑lyase subunit alpha/putative phage integrase IntZ |
| ? | NC_000913 | 2565489 = | 0 (0.000) | coding (1396/1404 nt) | eutA | ethanolamine ammonia‑lyase reactivase EutA | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 30 (0.710) | 27/490 | 0.4 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 4542049 | 0 (0.000) | coding (13/597 nt) | fimE | regulator for fimA | |||||