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 | 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 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 302,842 | T→A | intergenic (‑269/‑149) | paoA ← / → yagU | aldehyde dehydrogenase, Fe‑S subunit/DUF1440 domain‑containing inner membrane protein YagU |
| RA | 303,599 | C→T | N203N (AAC→AAT) | yagU → | DUF1440 domain‑containing inner membrane protein YagU |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 339,935 | C→T | A56V (GCC→GTC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,958 | G→A | D64N (GAC→AAC) | yahH → | putative uncharacterized protein YahH |
| RA | 366,339 | C→T | intergenic (‑34/+89) | lacZ ← / ← lacI | beta‑galactosidase/DNA‑binding transcriptional repressor LacI |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| JC JC | 788,785 | IS1 (+) +9 bp | coding (45‑53/1041 nt) | galM ← | galactose‑1‑epimerase |
| 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 | 1,293,196 | IS5 (–) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| JC JC | 1,293,196 | IS5 (+) +4 bp | intergenic (‑274/‑328) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| 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 | 1,337,394 | 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 |
| JC JC | 1,399,590 | IS5 (+) +4 bp | intergenic (‑64/+128) | fnr ← / ← ogt | DNA‑binding transcriptional dual regulator FNR/methylated‑DNA‑‑[protein]‑cysteine S‑methyltransferase |
| JC JC | 1,586,112 | IS3 (–) +3 bp | coding (373‑375/2280 nt) | ydeP ← | putative oxidoreductase YdeP |
| 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 | 1,829,887 | G→A | A293A (GCC→GCT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| 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 |
| 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 |
| 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 | 3,207,549 | 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 | 3,485,997 | IS2 (+) +5 bp | intergenic (‑179/‑119) | yhfA ← / → crp | OsmC family protein YhfA/DNA‑binding transcriptional dual regulator CRP |
| 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 | 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 | 4,400,254 | C→T | intergenic (+52/‑34) | miaA → / → hfq | tRNA dimethylallyltransferase/RNA‑binding protein Hfq |
| 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 |
| 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 | 280300 | 291377–290642 | 10343–11078 | 30 [29] | [29] 31 | yagB–insA3 | yagB,yagA,yagE,yagF,yagG,yagH,xynR,argF,argL,ykgS,insB3,insA3 |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 95 [0] | [0] 107 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423764–3424232 | 3424486–3424238 | 7–723 | 31 [29] | [28] 31 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 256107 | 25 (0.270) | 89 (0.980) | 59/572 | 0.2 | 82.3% | coding (131/459 nt) | gpt | xanthine‑guanine phsophoribosyltransferase |
| ? | NC_000913 | 371382 = | 14 (0.150) | coding (144/867 nt) | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase | |||||
| * | ? | NC_000913 | 315229 = | NA (NA) | 77 (0.830) +T |
53/586 | 0.4 | 78.6% | noncoding (1/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 3429986 = | 21 (0.230) | coding (38/258 nt) | yrdB | DUF1488 domain‑containing protein YrdB | |||||
| * | ? | NC_000913 | 1094245 = | NA (NA) | 80 (0.860) | 49/586 | 0.5 | 78.4% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 3429990 | 22 (0.240) | coding (34/258 nt) | yrdB | DUF1488 domain‑containing protein YrdB | |||||
| * | ? | NC_000913 | 1207790 = | 13 (0.140) | 65 (0.740) | 50/556 | 0.4 | 85.9% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.100) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.120) | 58 (0.660) | 43/556 | 0.7 | 85.7% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.100) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 94 (1.010) | 61/588 | 0.2 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 70 (0.750) | 47/588 | 0.6 | 66.0% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1667229 | 36 (0.390) | intergenic (‑10/+115) | bidA/mlc | dethiobiotin synthetase BidA/DNA‑binding transcriptional repressor Mlc | |||||
| * | ? | NC_000913 | 1619733 = | 111 (1.190) | 35 (0.380) | 28/588 | 2.0 | 24.0% | coding (160/384 nt) | marA | DNA‑binding transcriptional dual regulator MarA |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1651548 | NA (NA) | 83 (0.890) | 51/586 | 0.5 | 66.9% | noncoding (706/706 nt) | IS2 | repeat region |
| ? | NC_000913 | 1667225 = | 41 (0.440) | intergenic (‑6/+119) | bidA/mlc | dethiobiotin synthetase BidA/DNA‑binding transcriptional repressor Mlc | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 104 (1.120) | 71/588 | 0.1 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 74 (0.790) | 42/588 | 0.9 | 73.3% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2130694 = | 27 (0.290) | coding (185/1218 nt) | wcaD | colanic acid polymerase | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 97 (1.040) | 55/588 | 0.3 | 77.0% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2317112 = | 29 (0.310) | coding (2765/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 75 (0.800) | 50/588 | 0.5 | 77.3% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2130698 | 22 (0.240) | coding (181/1218 nt) | wcaD | colanic acid polymerase | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 68 (0.730) | 41/588 | 0.9 | 70.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2317116 | 29 (0.310) | coding (2761/2850 nt) | rcsC | histidine kinase RcsC | |||||
| * | ? | NC_000913 | 2170171 = | NA (NA) | 89 (0.950) | 57/588 | 0.3 | 72.4% | noncoding (1/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | = 2468300 | 34 (0.360) | coding (87/921 nt) | yfdH | bactoprenol glucosyl transferase | |||||
| * | ? | NC_000913 | = 2171428 | NA (NA) | 51 (0.550) | 37/586 | 1.2 | 60.7% | noncoding (1258/1258 nt) | IS3 | repeat region |
| ? | NC_000913 | 2468298 = | 33 (0.360) | coding (85/921 nt) | yfdH | bactoprenol glucosyl transferase | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 119 (1.280) | 75/588 | 0.1 | 79.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3653447 = | 31 (0.330) | pseudogene (212/478 nt) | yhiS | putative uncharacterized protein YhiS | |||||