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 | 29,113 | C→T | A247V (GCG→GTG) | dapB → | 4‑hydroxy‑tetrahydrodipicolinate reductase |
| RA | 73,675 | C→T | D283N (GAT→AAT) | thiP ← | thiamine ABC transporter membrane subunit |
| RA | 112,064 | (G)5→6 | coding (536/744 nt) | zapD ← | cell division factor ZapD |
| RA | 141,249 | T→C | intergenic (‑24/‑182) | gcd ← / → hpt | quinoprotein glucose dehydrogenase/hypoxanthine phosphoribosyltransferase |
| RA | 216,145 | (C)6→7 | intergenic (+166/+34) | nlpE → / ← yaeF | lipoprotein NlpE/peptidase C92 family protein |
| RA | 235,589 | A→G | R138R (CGT→CGC) | rnhA ← | ribonuclease HI |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 285,648 | C→G | A85G (GCC→GGC) | yagG → | putative D‑xylonate transporter YagG |
| RA | 296,079 | T→C | T340A (ACT→GCT) | intF ← | CP4‑6 prophage; putative phage integrase |
| RA | 353,345 | T→C | S214P (TCG→CCG) | prpE → | propionyl‑CoA synthetase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 505,624 | A→G | A237A (GCA→GCG) | ushA → | 5'‑nucleotidase/UDP‑sugar hydrolase |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 628,758 | A→G | T70A (ACG→GCG) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| RA | 650,305 | C→T | A62A (GCG→GCA) | citE ← | citrate lyase beta subunit |
| RA | 656,905 | A→G | T117A (ACC→GCC) | pagP → | Lipid IVA palmitoyltransferase |
| RA | 736,692 | T→A | I83N (ATC→AAC) | ybfQ → | inactive transposase YbfQ |
| RA | 784,602 | A→G | P74P (CCT→CCC) | zitB ← | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter |
| RA | 801,638 | A→G | T294A (ACC→GCC) | ybhH → | putative isomerase YbhH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 972,194 | A→G | Y148C (TAC→TGC) | ycbJ → | putative phosphotransferase YcbJ |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,012,766 | A→G | T256A (ACA→GCA) | pqiA → | intermembrane transport protein PqiA |
| RA | 1,064,754 | A→G | N240S (AAC→AGC) | yccE → | uncharacterized protein YccE |
| RA | 1,070,255 | A→G | F34L (TTC→CTC) | rutF ← | flavin reductase |
| RA | 1,108,598 | C→T | G115E (GGA→GAA) | opgC ← | protein required for succinyl modification of osmoregulated periplasmic glucans |
| RA | 1,134,318 | C→T | R173C (CGC→TGC) | flgF → | flagellar basal‑body rod protein FlgF |
| RA | 1,136,668 | A→G | Q132R (CAG→CGG) | flgI → | flagellar P‑ring protein |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,212,844 | A→G | F88F (TTT→TTC) | ycgX ← | uncharacterized protein YcgX |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,225,091 | T→C | T91A (ACA→GCA) | minD ← | Z‑ring positioning protein MinD |
| RA | 1,243,642 | C→T | R155W (CGG→TGG) | emtA → | lytic murein transglycosylase E |
| RA | 1,276,290 | C→T | A443A (GCG→GCA) | narX ← | sensory histidine kinase NarX |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,351,196 | (G)7→6 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,380,309 | G→A | R54R (CGG→CGA) | ycjU → | beta‑phosphoglucomutase |
| RA | 1,380,989 | A→G | pseudogene (169/969 nt) | ycjV → | putative ABC transporter ATP‑binding protein YcjV |
| RA | 1,403,881 | T→C | T229A (ACC→GCC) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,477,669 | A→G | T17A (ACG→GCG) | ynbA → | putative inner membrane protein |
| RA | 1,483,868 | A→G | T270A (ACC→GCC) | hrpA → | ATP‑dependent RNA helicase HrpA |
| 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 | 1,604,249 | C→T | T68I (ACC→ATC) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,632,712 | A→G | intergenic (‑427/‑178) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| 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 | 1,729,457 | T→C | V124A (GTC→GCC) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,731,538 | T→C | Y818H (TAT→CAT) | lhr → | putative ATP‑dependent helicase Lhr |
| RA | 1,752,947 | G→A | P295L (CCG→CTG) | ydhV ← | putative oxidoreductase |
| RA | 1,759,757 | A→T | I256N (ATC→AAC) | sufS ← | L‑cysteine desulfurase |
| RA | 1,804,810 | (A)7→8 | pseudogene (1717/1900 nt) | arpB → | putative ankyrin repeat protein B, N‑terminal fragment |
| RA | 1,818,550 | (C)7→8 | intergenic (‑50/+55) | chbF ← / ← chbR | monoacetylchitobiose‑6‑phosphate hydrolase/DNA‑binding transcriptional dual regulator ChbR |
| RA | 1,825,038 | (T)7→6 | intergenic (‑101/+102) | ves ← / ← spy | HutD family protein Ves/ATP‑independent periplasmic chaperone |
| RA | 1,868,501 | T→C | S532P (TCT→CCT) | yeaG → | protein kinase YeaG |
| 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 | 1,922,957 | C→T | A5T (GCG→ACG) | pphA ← | phosphoprotein phosphatase 1 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,010,036 | G→A | P72P (CCG→CCA) | yedK → | putative SOS response‑associated peptidase YedK |
| RA | 2,058,429 | G→A | A473V (GCC→GTC) | yeeO ← | FMN/FAD exporter |
| RA | 2,062,244 | G→A | intergenic (‑311/‑16) | nac ← / → asnV | DNA‑binding transcriptional dual regulator Nac/tRNA‑Asn |
| RA | 2,079,625 | T→C | T323A (ACA→GCA) | yeeA ← | putative transporter YeeA |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,257,400 | A→G | intergenic (‑65/+29) | psuT ← / ← psuG | putative pseudouridine transporter/pseudouridine‑5'‑phosphate glycosidase |
| RA | 2,260,229 | (C)5→6 | coding (1182/1692 nt) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,312,788 | (T)6→5 | intergenic (‑39/‑296) | ompC ← / → micF | outer membrane porin C/small regulatory RNA MicF |
| RA | 2,334,980 | T→C | L555L (CTA→CTG) | yfaA ← | DUF2138 domain‑containing protein YfaA |
| RA | 2,425,505 | Δ1 bp | coding (412/687 nt) | hisQ ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,480,626 | (C)5→4 | intergenic (+96/+12) | dsdA → / ← emrY | D‑serine ammonia‑lyase/tripartite efflux pump membrane subunit EmrY |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,656,884 | T→C | E67G (GAG→GGG) | fdx ← | reduced ferredoxin |
| RA | 2,671,549 | T→C | F109L (TTC→CTC) | hcaB → | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| RA | 2,776,823 | T→C | V146V (GTT→GTC) | yfjY → | CP4‑57 prophage; RadC‑like JAB domain‑containing protein YfjY |
| RA | 2,776,881 | G→A | R2K (AGA→AAA) | ypjJ → | CP4‑57 prophage; DUF987 domain‑containing protein YpjJ |
| RA | 2,776,957 | A→C | G27G (GGA→GGC) | ypjJ → | CP4‑57 prophage; DUF987 domain‑containing protein YpjJ |
| RA | 2,776,963 | T→C | Y29Y (TAT→TAC) | ypjJ → | CP4‑57 prophage; DUF987 domain‑containing protein YpjJ |
| RA | 2,777,002 | T→C | D42D (GAT→GAC) | ypjJ → | CP4‑57 prophage; DUF987 domain‑containing protein YpjJ |
| 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 | 2,881,629 | T→C | M172V (ATG→GTG) | casC ← | type I‑E CRISPR system Cascade subunit CasC |
| RA | 2,903,129 | (G)5→6 | coding (1234/1479 nt) | ygcE → | putative sugar kinase YgcE |
| RA | 2,903,312 | T→C | Y473H (TAT→CAT) | ygcE → | putative sugar kinase YgcE |
| RA | 2,909,358 | T→C | E103E (GAA→GAG) | pyrG ← | CTP synthetase |
| RA | 2,945,671 | T→C | T58A (ACG→GCG) | tcdA ← | tRNA threonylcarbamoyladenosine dehydratase |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,965,981 | T→C | G19G (GGA→GGG) | lgt ← | phosphatidylglycerol‑‑prolipoprotein diacylglyceryl transferase |
| RA | 3,006,504 | G→A | A81A (GCG→GCA) | ygeW → | putative carbamoyltransferase YgeW |
| RA | 3,009,674 | G→A | G304D (GGC→GAC) | ygeY → | putative peptidase YgeY |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,076,414 | G→A | A348V (GCG→GTG) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,158,617 | G→A | intergenic (+41/‑10) | yqhG → / → yqhH | DUF3828 domain‑containing protein YqhG/lipoprotein YqhH |
| RA | 3,280,999 | T→C | pseudogene (299/402 nt) | agaW → | N‑acetyl‑D‑galactosamine specific PTS truncated enzyme IIC component |
| RA | 3,297,909 | A→G | V77A (GTA→GCA) | yraQ ← | permease family protein YraQ |
| RA | 3,298,668 | G→A | T60I (ACC→ATC) | yraR ← | putative nucleoside‑diphosphate‑sugar epimerase |
| RA | 3,316,522 | T→C | E335E (GAA→GAG) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,334,717 | T→C | intergenic (+36/‑192) | ispB → / → sfsB | all‑trans‑octaprenyl‑diphosphate synthase/putative transcriptional regulator SfsB |
| RA | 3,336,470 | G→A | P9S (CCA→TCA) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,348,177 | A→G | Q71R (CAG→CGG) | npr → | phosphorelay protein Npr |
| RA | 3,350,364 | G→A | S32S (AGC→AGT) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,476,286 | T→C | H52R (CAC→CGC) | yheO ← | putative DNA‑binding transcriptional regulator YheO |
| RA | 3,477,136 | T→C | D95G (GAC→GGC) | fkpA ← | peptidyl‑prolyl cis‑trans isomerase FkpA |
| RA | 3,546,895 | T→C | F113L (TTC→CTC) | gntT → | high‑affinity gluconate transporter |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,727,522 | C→T | G76D (GGT→GAT) | yiaB ← | conserved inner membrane protein YiaB |
| RA | 3,767,673 | T→C | pseudogene (453/702 nt) | yibJ → | putative RHS domain‑containing protein YibJ |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,845,884 | C→T | A428A (GCG→GCA) | uhpT ← | hexose‑6‑phosphate:phosphate antiporter |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,977,855 | (G)6→7 | coding (331/1080 nt) | rffT → | 4‑acetamido‑4,6‑dideoxy‑D‑galactose transferase |
| RA | 3,999,267 | A→G | T429A (ACA→GCA) | uvrD → | ssDNA translocase and dsDNA helicase ‑ DNA helicase II |
| RA | 4,238,183 | A→G | S184G (AGC→GGC) | yjbH → | YjbH family protein |
| RA | 4,276,536 | C→T | R356C (CGC→TGC) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,285,533 | A→G | R613R (CGT→CGC) | acs ← | acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,350,361 | C→T | T434T (ACG→ACA) | dcuS ← | sensory histidine kinase DcuS |
| RA | 4,352,791 | A→G | I70V (ATC→GTC) | ghoS → | antitoxin of the GhoTS toxin‑antitoxin system |
| RA | 4,390,086 | A→G | V92A (GTT→GCT) | psd ← | phosphatidylserine decarboxylase proenzyme |
| RA | 4,403,940 | A→G | N214S (AAC→AGC) | hflC → | regulator of FtsH protease |
| RA | 4,410,053 | (T)9→10 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,422,530 | T→C | G115G (GGT→GGC) | ulaD → | 3‑keto‑L‑gulonate‑6‑phosphate decarboxylase UlaD |
| RA | 4,430,919 | T→C | C352C (TGT→TGC) | cycA → | serine/alanine/glycine/cycloserine:H(+)symporter |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,522,746 | A→G | V450A (GTG→GCG) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | 4,541,580 | A→G | intergenic (+21/‑457) | fimB → / → fimE | regulator for fimA/regulator for fimA |
| RA | 4,549,889 | T→C | intergenic (+179/+64) | fimH → / ← gntP | type 1 fimbriae D‑mannose specific adhesin/fructuronate transporter |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1311182 | 1311210 | 29 | 3 [1] | [1] 2 | tonB | Ton complex subunit TonB |
| * | * | ÷ | NC_000913 | 1996898 | 1997017 | 120 | 2 [1] | [1] 2 | [sdsN] | [sdsN] |
| * | * | ÷ | NC_000913 | 2033819 | 2033897 | 79 | 2 [1] | [1] 4 | rseX/yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 2619667 | 2619682 | 16 | 2 [1] | [1] 2 | uraA | hypothetical protein |
| * | * | ÷ | NC_000913 | 3423796–3424234 | 3424517–3424242 | 9–722 | 2 [1] | [0] 2 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3751944 | 3751981 | 38 | 3 [1] | [1] 2 | yiaT/yiaU | outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU |
| * | * | ÷ | NC_000913 | 3793725 | 3793727 | 3 | 2 [0] | [0] 2 | htrL/rfaD | protein HtrL/ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase |
| * | * | ÷ | NC_000913 | 3944174–3945565 | 3946839–3946697 | 1133–2666 | 2 [1] | [1] 3 | [rrlC]–rrfC | [rrlC],rrfC |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 19 (0.920) | 32 (1.550) | 25/272 | 0.1 | 77.2% | 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) | 26 (1.250) | 18/274 | 0.2 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||