mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 93,282 | A→G | V39V (GTA→GTG) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 166,619 | C→T | S630S (AGC→AGT) | mrcB → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcB |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,975 | T→C | L194P (CTG→CCG) | yagG → | putative D‑xylonate transporter YagG |
| RA | 372,274 | C→T | R54C (CGT→TGT) | mhpD → | 2‑hydroxypentadienoate hydratase |
| RA | 375,075 | G→A | intergenic (+194/‑384) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 375,168 | G→A | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 388,689 | A→G | intergenic (+43/+64) | tauD → / ← hemB | taurine dioxygenase/porphobilinogen synthase |
| RA | 410,898 | (G)6→8 | coding (755/909 nt) | mak → | manno(fructo)kinase |
| RA | 416,658 | A→G | F99L (TTC→CTC) | sbcD ← | ATP dependent, structure specific DNA nuclease ‑ SbcD subunit |
| RA | 469,571 | (A)8→7 | coding (701/1773 nt) | mdlA → | ABC transporter family protein MdlA |
| RA | 517,173 | A→G | L197L (TTA→TTG) | fetB → | putative iron ABC exporter membrane subunit FetB |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 635,374 | (C)5→6 | coding (3/630 nt) coding (1196/1221 nt) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 877,873 | A→G | F55L (TTT→CTT) | rimO ← | ribosomal protein S12 methylthiotransferase RimO |
| RA | 881,516 | (G)5→4 | coding (790/1203 nt) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 900,696 | (A)6→5 | intergenic (‑121/+170) | artJ ← / ← artM | L‑arginine ABC transporter periplasmic binding protein/L‑arginine ABC transporter membrane subunit ArtM |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 1,001,023 | (A)8→7 | coding (1808/2601 nt) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,002,435 | A→G | Y210C (TAC→TGC) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,026,812 | (C)6→7 | coding (204/459 nt) | mgsA ← | methylglyoxal synthase |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,167,510 | C→T | intergenic (+121/‑89) | ndh → / → ycfJ | NADH:quinone oxidoreductase II/PF05433 family protein YcfJ |
| RA | 1,199,794 | C→T | R338H (CGT→CAT) | intE ← | e14 prophage; putative integrase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,243,195 | T→C | F6L (TTT→CTT) | emtA → | lytic murein transglycosylase E |
| RA | 1,258,755 | T→C | intergenic (‑242/‑36) | pth ← / → ychH | peptidyl‑tRNA hydrolase/stress‑induced protein |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,390,618 | A→G | intergenic (‑20/+62) | mpaA ← / ← ymjC | murein tripeptide amidase A/putative uncharacterized protein YmjC |
| RA | 1,398,183 | T→C | D147G (GAC→GGC) | uspE ← | universal stress protein with a role cellular motility |
| RA | 1,455,774 | A→G | N204S (AAC→AGC) | paaC → | phenylacetyl‑CoA 1,2‑epoxidase, structural subunit |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,865,878 | G→A | L199L (CTG→TTG) | mipA ← | scaffolding protein that interacts with murein polymerase and murein hydrolase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,894,349 | (A)8→9 | coding (217/300 nt) | yoaC → | DUF1889 domain‑containing protein YoaC |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,120,438 | (C)6→7 | coding (1117/1395 nt) | wcaJ ← | undecaprenyl‑phosphate glucose phosphotransferase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,260,472 | A→G | G313G (GGT→GGC) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,346,909 | T→C | V682A (GTG→GCG) | nrdA → | ribonucleoside‑diphosphate reductase 1 subunit alpha |
| RA | 2,357,354 | A→G | T151A (ACC→GCC) | rpnE → | inactive recombination‑promoting nuclease‑like protein RpnE |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,472,123 | A→G | Y89H (TAC→CAC) | yfdM ← | CPS‑53 (KpLE1) prophage; putative methyltransferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,531,168 | T→C | V22V (GTA→GTG) | zipA ← | cell division protein ZipA |
| RA | 2,636,776 | T→C | D194G (GAC→GGC) | der ← | 50S ribosomal subunit stability factor |
| RA | 2,638,945 | +C | coding (339/621 nt) | yfgM ← | ancillary SecYEG translocon subunit |
| RA | 2,708,823 | C→T | E194E (GAG→GAA) | rseA ← | anti‑sigma factor |
| RA | 2,734,535 | T→C | E167G (GAG→GGG) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,748,516 | G→A | V185V (GTG→GTA) | ypjD → | cytochrome c assembly family protein |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,919,458 | A→G | L430P (CTG→CCG) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,933,613 | T→C | T26A (ACA→GCA) | fucA ← | L‑fuculose‑phosphate aldolase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,953,004 | T→C | A1000A (GCA→GCG) | recB ← | exodeoxyribonuclease V subunit RecB |
| RA | 2,983,172 | C→T | G29G (GGG→GGA) | kduD ← | putative 2‑keto‑3‑deoxy‑D‑gluconate dehydrogenase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,080,917 | A→G | L240P (CTG→CCG) | tktA ← | transketolase 1 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,379,582 | A→G | V139A (GTG→GCG) | zapE ← | cell division factor ZapE with ATPase activity |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,603,930 | A→G | V105A (GTG→GCG) | ftsY ← | signal recognition particle receptor |
| RA | 3,765,830 | G→A | R1216R (CGG→CGA) | rhsA → | rhs element protein RhsA |
| RA | 3,778,740 | T→C | F448L (TTC→CTC) | lldP → | lactate/glycolate:H(+) symporter LldP |
| RA | 3,795,673 | (G)5→6 | coding (745/1047 nt) | waaF → | ADP‑heptose‑‑LPS heptosyltransferase 2 |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,863,695 | A→G | intergenic (‑92/‑204) | glvC ← / → yidP | putative PTS enzyme II component GlvC/putative DNA‑binding transcriptional regulator YidP |
| RA | 3,879,282 | T→C | T280A (ACT→GCT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,886,269 | C→T | G398G (GGC→GGT) | yidC → | membrane protein insertase YidC |
| RA | 3,995,912 | C→T | H110H (CAC→CAT) | yigA → | conserved protein YigA |
| RA | 4,026,764 | C→T | R80C (CGC→TGC) | fre → | flavin reductase |
| RA | 4,230,839 | A→G | T162T (ACA→ACG) | rluF → | 23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase |
| RA | 4,241,586 | A→G | S223S (AGT→AGC) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,252,781 | T→C | R92R (CGT→CGC) | ubiC → | chorismate lyase |
| RA | 4,276,134 | C→T | R222C (CGC→TGC) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,376,552 | T→C | intergenic (+110/‑1) | ecnA → / → ecnB | entericidin A lipoprotein, antidote to entericidin B/bacteriolytic entericidin B lipoprotein |
| RA | 4,422,901 | A→G | E19G (GAG→GGG) | ulaE → | L‑ribulose‑5‑phosphate 3‑epimerase UlaE |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,455,044 | A→G | L189P (CTG→CCG) | fbp ← | fructose‑1,6‑bisphosphatase 1 |
| RA | 4,482,705 | A→G | L378P (CTG→CCG) | valS ← | valine‑‑tRNA ligase |
| RA | 4,569,443 | A→G | pseudogene (446/921 nt) | rpnD → | truncated recombination‑promoting nuclease‑like protein RpnD |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,609,336 | (C)7→8 | intergenic (+13/‑78) | yjjG → / → prfC | pyrimidine nucleotidase/peptide chain release factor RF3 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 223639–223740 | 224665–223742 | 3–1027 | 9 [7] | [7] 8 | [rrsH] | [rrsH] |
| * | * | ÷ | NC_000913 | 732922–732955 | 734737–734685 | 1731–1816 | 8 [7] | [7] 8 | [rhsC]–[ybfO] | [rhsC],ybfB,[ybfO] |
| * | * | ÷ | NC_000913 | 3423791–3424234 | 3424523–3424239 | 6–733 | 8 [4] | [6] 8 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3762322–3764072 | 3765218–3764077 | 6–2897 | 8 [7] | [7] 9 | rhsA | rhs element protein RhsA |
| * | * | ÷ | NC_000913 | 3765338–3765391 | 3765774–3765674 | 284–437 | 8 [6] | [7] 8 | rhsA | rhs element protein RhsA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 15 (0.610) | 9/190 | 1.4 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 19 (0.770) | 15/190 | 0.6 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 12 (0.340) +T |
10/274 | 2.1 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 3363001 = | 47 (1.310) | 48 (1.340) | 33/274 | 0.2 | 67.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 46 (1.280) | 33/276 | 0.2 | 97.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4542690 | 41 (1.140) | 9 (0.270) | 8/258 | 2.3 | 20.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 33 (0.980) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||