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 |
| MC JC | 59,092 | (15-bp)2→1 | coding (619‑633/651 nt) | yabP → | putative uncharacterized protein YabP |
| RA | 100,946 | T→C | M61T (ATG→ACG) | murC → | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| MC JC | 366,181 | Δ93 bp | coding (33‑125/3075 nt) | lacZ ← | beta‑galactosidase |
| RA | 367,573 | G→A | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor LacI/DNA‑binding transcriptional activator MhpR |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| JC JC | 788,785 | IS1 (+) +9 bp | coding (45‑53/1041 nt) | galM ← | galactose‑1‑epimerase |
| 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 | 1,424,309 | A→G | K176K (AAA→AAG) | trkG → | K(+) transporter TrkG |
| JC JC | 1,633,132 | IS5 (+) +4 bp | coding (61‑64/234 nt) | ydfK → | cold shock protein YdfK |
| 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 |
| RA | 1,728,514 | C→A | T56T (ACC→ACA) | rnt → | ribonuclease T |
| 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 | 1,979,509 | IS30 (+) +2 bp | intergenic (‑294/‑243) | 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 | 2,174,205 | IS1 (+) +9 bp | intergenic (‑1332/+69) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,187,650 | IS1 (–) +9 bp | coding (757‑765/1035 nt) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,237,235 | C→T | Q173Q (CAG→CAA) | mglC ← | D‑galactose/methyl‑galactoside ABC transporter membrane subunit |
| RA | 2,331,496 | C→A | intergenic (‑1699/+2840) | yfaQ ← / ← yfaT | tandem DUF2300 domain‑containing protein YfaQ/DUF1175 domain‑containing protein YfaT |
| 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 | 2,877,914 | C→G | intergenic (+296/+655) | iap → / ← cas2 | alkaline phosphatase isozyme conversion protein/CRISPR‑associated endoribonuclease Cas2 |
| 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 | 3,266,159 | A→C | C303G (TGT→GGT) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,266,469 | C→A | L199F (TTG→TTT) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| 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 | 3,474,425 | T→C | K43R (AAA→AGA) | rpsL ← | 30S ribosomal subunit protein S12 |
| 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 | 3,571,755 | C→T | S583N (AGC→AAC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| 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 |
| JC | 3,854,774 | (GGCT)2→1 | coding (853‑856/1185 nt) | emrD → | multidrug efflux pump EmrD |
| RA | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| 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 | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| 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 | 4,392,725 | C→T | intergenic (+67/‑167) | glyY → / → yjeV | tRNA‑Gly/uncharacterized protein YjeV |
| RA | 4,400,254 | C→T | intergenic (+52/‑34) | miaA → / → hfq | tRNA dimethylallyltransferase/RNA‑binding protein Hfq |
| RA | 4,423,337 | C→T | S164S (TCC→TCT) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,449,586 | G→A | P23S (CCG→TCG) | ppa ← | inorganic pyrophosphatase |
| 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 | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| JC JC | 4,541,967 | IS5 (–) +4 bp | intergenic (+408/‑67) | fimB → / → fimE | Type 1 fimbriae regulatory protein FimB/regulator for fimA |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| 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 | 258678 | 258683 | 6 | 5 [0] | [0] 55 | crl | RNA polymerase holoenzyme assembly factor Crl |
| * | * | ÷ | NC_000913 | 3423884–3424234 | 3424414–3424238 | 5–531 | 5 [4] | [4] 5 | rrlD | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 256107 | 120 (2.050) | 61 (1.080) | 59/468 | 0.1 | 41.6% | coding (131/459 nt) | gpt | xanthine‑guanine phsophoribosyltransferase |
| ? | NC_000913 | 371382 = | 55 (0.970) | coding (144/867 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase | |||||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 55 (0.970) | 49/468 | 0.3 | 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 | = 676346 | 13 (0.230) | 37 (0.640) | 36/476 | 0.6 | 74.0% | coding (202/978 nt) | ybeQ | Sel1 repeat‑containing protein YbeQ |
| ? | NC_000913 | 687851 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 30 (0.510) | 19 (0.350) | 18/452 | 1.4 | 46.3% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 16 (0.290) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 30 (0.510) | 14 (0.260) | 14/452 | 1.8 | 38.9% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 16 (0.290) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1978502 | 6 (0.100) | 13 (0.230) | 13/468 | 2.0 | 81.8% | 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 | = 4542690 | 7 (0.120) | 12 (0.210) | 12/466 | 2.1 | 53.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 14 (0.250) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||