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 | 24,855 | T→C | V822A (GTC→GCC) | ileS → | isoleucine‑‑tRNA ligase |
RA | 39,897 | A→G | Y164H (TAC→CAC) | caiA ← | crotonobetainyl‑CoA reductase |
RA | 136,976 | C→T | intergenic (‑59/‑107) | yacC ← / → cueO | putative lipoprotein YacC/cuprous oxidase/multicopper oxidase with role in copper homeostasis |
RA | 156,532 | A→G | S118P (TCT→CCT) | yadN ← | putative fimbrial protein YadN |
RA | 177,992 | A→G | R157R (CGT→CGC) | btuF ← | vitamin B12 ABC transporter periplasmic binding protein |
RA | 208,270 | A→G | I1049V (ATC→GTC) | dnaE → | DNA polymerase III subunit alpha |
RA | 239,358 | G→A | pseudogene (169/189 nt) | yafF → | putative uncharacterized protein YafF |
MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
RA | 289,143 | A→G | V7A (GTT→GCT) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
RA | 312,889 | A→G | intergenic (‑112/+252) | ykgM ← / ← ykgR | putative ribosomal protein/putative membrane protein YkgR |
RA | 351,991 | C→T | D259D (GAC→GAT) | prpD → | 2‑methylcitrate dehydratase |
RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
RA | 424,328 | A→G | N604S (AAC→AGC) | malZ → | maltodextrin glucosidase |
RA | 431,476 | T→C | N180D (AAC→GAC) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
RA | 438,606 | C→T | S524S (TCG→TCA) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
RA | 443,048 | A→G | intergenic (+51/+3) | thiI → / ← yajL | tRNA uridine 4‑sulfurtransferase/protein/nucleic acid deglycase 3 |
RA | 493,593 | T→C | L501P (CTG→CCG) | dnaX → | DNA polymerase III subunit tau |
RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
RA | 530,868 | A→G | L120P (CTG→CCG) | selU ← | tRNA 2‑selenouridine synthase |
RA | 565,116 | A→G | V288A (GTC→GCC) | intD ← | DLP12 prophage; putative integrase |
RA | 621,652 | A→G | L180L (TTG→CTG) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
RA | 662,772 | A→G | F398L (TTC→CTC) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase DacA |
RA | 683,597 | A→G | G272G (GGT→GGC) | rihA ← | pyrimidine‑specific ribonucleoside hydrolase RihA |
RA | 709,867 | C→T | D26D (GAC→GAT) | chiQ → | lipoprotein ChiQ |
RA | 725,753 | G→A | A428A (GCC→GCT) | kdpB ← | K(+) transporting P‑type ATPase subunit KdpB |
RA | 749,869 | A→G | G767G (GGT→GGC) | ybgQ ← | putative fimbrial usher protein YbgQ |
RA | 763,438 | A→G | H142R (CAC→CGC) | sucC → | succinyl‑CoA synthetase subunit beta |
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 | 955,270 | A→G | S455P (TCG→CCG) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor YcaO |
RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
RA | 1,048,830 | T→C | E168G (GAG→GGG) | gfcB ← | lipoprotein GfcB |
RA | 1,050,469 | A→G | K148R (AAA→AGA) | insB‑4 → | IS1 protein InsB |
RA | 1,061,528 | A→G | D758G (GAC→GGC) | torA → | trimethylamine N‑oxide reductase 1 |
RA | 1,073,736 | C→T | G92G (GGG→GGA) | rutA ← | pyrimidine oxygenase |
RA | 1,100,317 | G→A | A8T (GCA→ACA) | ycdZ → | putative inner membrane protein |
RA | 1,106,515 | A→G | D54G (GAC→GGC) | clsC → | cardiolipin synthase C |
RA | 1,121,290 | A→G | I66I (ATT→ATC) | dinI ← | DNA damage‑inducible protein I |
RA | 1,122,081 | A→G | F176S (TTT→TCT) | pyrC ← | dihydroorotase |
RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
RA | 1,144,436 | A→G | intergenic (‑69/‑66) | rne ← / → yceQ | ribonuclease E/DUF2655 domain‑containing protein YceQ |
RA | 1,169,369 | (T)6→5 | intergenic (+39/+43) | bhsA → / ← ldtC | DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA/L,D‑transpeptidase YcfS |
RA | 1,187,531 | G→T | A237D (GCT→GAT) | roxA ← | ribosomal protein‑arginine oxygenase |
RA | 1,190,235 | A→G | V71V (GTT→GTC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
RA | 1,212,088 | (C)8→9 | intergenic (‑85/+172) | iraM ← / ← ymgK | anti‑adaptor protein IraM, inhibitor of sigma(S) proteolysis/protein YmgK |
RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
RA | 1,226,800 | A→G | L67L (TTA→TTG) | ycgJ → | PF05666 family protein YcgJ |
RA | 1,251,954 | A→G | T297A (ACC→GCC) | dhaR → | DNA‑binding transcriptional dual regulator DhaR |
RA | 1,272,570 | T→C | S22P (TCA→CCA) | chaC → | glutathione‑specific gamma‑glutamylcyclotransferase |
RA | 1,283,380 | C→T | P1173S (CCT→TCT) | narG → | nitrate reductase A subunit alpha |
RA | 1,400,333 | (A)5→6 | coding (1441/1527 nt) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
RA | 1,403,700 | A→G | V289A (GTT→GCT) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
RA | 1,409,337 | T→C | P10P (CCT→CCC) | ynaL → | protein YnaL |
RA | 1,509,166 | T→C | intergenic (‑102/‑120) | yncJ ← / → hicA | protein YncJ/toxin of the HicA‑HicB toxin‑antitoxin system |
RA | 1,527,395 | A→G | intergenic (+243/‑495) | yncH → / → rhsE | DUF5445 domain‑containing protein YncH/RhsE protein in rhs element |
RA | 1,531,315 | A→C | pseudogene (730/1054 nt) | yncI → | putative transposase YncI |
RA | 1,532,727 | T→C | H304H (CAT→CAC) | ydcC → | H repeat‑associated putative transposase YdcC |
RA | 1,532,746 | T→A | W311R (TGG→AGG) | ydcC → | H repeat‑associated putative transposase YdcC |
RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
RA | 1,555,722 | C→T | intergenic (‑53/+104) | maeA ← / ← sra | malate dehydrogenase, NAD‑requiring/30S ribosomal subunit protein S22 |
RA | 1,597,313 | (C)7→8 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
RA | 1,631,684 | G→A | A201V (GCA→GTA) | ydfJ ← | putative transporter YdfJ |
RA | 1,632,949 | C→T | A20A (GCC→GCT) | ynfT → | Qin prophage; protein YnfT |
RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
RA | 1,676,056 | C→T | G102D (GGC→GAC) | pntB ← | pyridine nucleotide transhydrogenase subunit beta |
RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide/tripeptide:H(+) symporter DtpA/glutathione S‑transferase GstA |
RA | 1,721,368 | A→G | T35T (ACA→ACG) | ydhJ → | putative membrane fusion protein YdhJ |
RA | 1,784,834 | T→C | D760G (GAC→GGC) | ppsA ← | phosphoenolpyruvate synthetase |
RA | 1,803,246 | G→A | pseudogene (153/1900 nt) | arpB → | putative ankyrin repeat protein B, N‑terminal fragment |
RA | 1,870,782 | T→C | I133T (ATC→ACC) | cdgI → | putative c‑di‑GMP binding protein CdgI |
RA | 1,870,791 | T→C | V136A (GTT→GCT) | cdgI → | putative c‑di‑GMP binding protein CdgI |
RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
RA | 1,874,546 | (C)5→6 | coding (195/447 nt) | yeaL → | conserved inner membrane protein YeaL |
RA | 1,878,801 | T→C | V10A (GTA→GCA) | yoaK → | putative membrane protein YoaK |
JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
RA | 1,901,041 | T→C | H182R (CAC→CGC) | yoaE ← | putative inner membrane protein |
RA | 1,917,003 | Δ1 bp | coding (746/1284 nt) | yebS → | intermembrane transport protein YebS |
RA | 1,971,486 | A→G | R402R (CGT→CGC) | tar ← | methyl‑accepting chemotaxis protein Tar |
MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
RA | 2,003,639 | A→G | intergenic (‑33/‑233) | fliC ← / → fliD | flagellar filament structural protein/flagellar filament capping protein |
RA | 2,016,955 | (C)5→6 | coding (402/1374 nt) | fliI → | flagellum‑specific ATP synthase FliI |
RA | 2,032,094 | A→G | L75S (TTA→TCA) | dcm ← | DNA‑cytosine methyltransferase |
RA | 2,067,300 | C→T | G8R (GGA→AGA) | insH‑6 ← | CP4‑44 prophage; IS5 transposase and trans‑activator |
RA | 2,114,296 | G→A | A11V (GCG→GTG) | galF ← | UTP:glucose‑1‑phosphate uridylyltransferase, low activity |
RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
RA | 2,174,939 | T→C | P37P (CCA→CCG) | gatA ← | galactitol‑specific PTS enzyme IIA component |
RA | 2,192,803 | T→C | intergenic (‑7/+256) | yehE ← / ← mrp | DUF2574 domain‑containing protein YehE/P‑loop NTPase family protein |
RA | 2,201,201 | T→C | V308A (GTC→GCC) | yehI → | DUF4132 domain‑containing protein YehI |
RA | 2,258,987 | T→C | T104A (ACC→GCC) | psuK ← | putative pseudouridine kinase |
RA | 2,280,240 | T→C | T82A (ACG→GCG) | rsuA ← | 16S rRNA pseudouridine(516) synthase |
RA | 2,299,723 | T→C | T180A (ACG→GCG) | napG ← | ferredoxin‑type protein NapG |
RA | 2,319,449 | T→C | N143S (AAC→AGC) | rcsC ← | sensory histidine kinase RcsC |
RA | 2,370,965 | T→C | L20L (TTA→CTA) | arnT → | lipid IVA 4‑amino‑4‑deoxy‑L‑arabinosyltransferase |
RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
RA | 2,447,800 | T→C | E214G (GAA→GGA) | prmB ← | 50S ribosomal subunit protein L3 N(5)‑glutamine methyltransferase |
RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
RA | 2,599,252 | A→G | V170A (GTA→GCA) | dapA ← | 4‑hydroxy‑tetrahydrodipicolinate synthase |
RA | 2,606,033 | A→G | E408G (GAG→GGG) | hyfD → | hydrogenase 4 component D |
RA | 2,663,526 | G→A | V29I (GTA→ATA) | suhB → | inositol‑phosphate phosphatase |
RA | 2,674,580 | (T)7→8 | coding (109/873 nt) | yphB ← | putative aldose 1‑epimerase YphB |
RA | 2,703,698 | G→A | G122G (GGC→GGT) | rnc ← | RNase III |
RA | 2,734,543 | (C)8→10 | coding (492/732 nt) | pgeF ← | polyphenol oxidase YfiH |
RA | 2,767,153 | G→A | G57D (GGT→GAT) | rnlB → | CP4‑57 prophage; antitoxin RnlB |
RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
RA | 2,814,455 | A→G | G93G (GGT→GGC) | luxS ← | S‑ribosylhomocysteine lyase |
RA | 2,853,222 | T→C | W363R (TGG→CGG) | hypD → | Fe‑(CN)2CO cofactor assembly scaffold protein HypD |
RA | 2,854,143 | G→A | G297E (GGG→GAG) | hypE → | hydrogenase maturation protein, carbamoyl dehydratase |
MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
RA | 2,881,094 | A→G | L350S (TTA→TCA) | casC ← | type I‑E CRISPR system Cascade subunit CasC |
RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
RA | 2,973,764 | T→C | L33L (CTA→CTG) | lplT ← | lysophospholipid transporter |
RA | 2,977,087 | T→C | G163G (GGT→GGC) | galR → | DNA‑binding transcriptional dual regulator GalR |
RA | 2,980,423 | T→C | L71L (TTA→TTG) | ygeA ← | amino acid racemase |
RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
RA | 3,091,562 | T→C | G143G (GGT→GGC) | rsmE → | 16S rRNA m(3)U1498 methyltransferase |
RA | 3,144,785 | T→C | N119S (AAC→AGC) | hybA ← | hydrogenase 2 iron‑sulfur protein |
RA | 3,196,669 | T→C | T29A (ACC→GCC) | rfaE ← | fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase |
RA | 3,229,464 | A→G | T193A (ACC→GCC) | ygjK → | glycoside hydrolase |
RA | 3,270,481 | T→C | noncoding (112/377 nt) | rnpB ← | RNase P catalytic RNA component |
RA | 3,290,285 | A→G | D491G (GAC→GGC) | yraJ → | putative fimbrial usher protein YraJ |
RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
RA | 3,366,694 | T→C | T9A (ACA→GCA) | insH‑10 ← | IS5 transposase and trans‑activator |
RA | 3,385,829 | G→A | intergenic (+28/+28) | yhcN → / ← yhcO | DUF1471 domain‑containing stress‑induced protein YhcN/putative barnase inhibitor |
RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
RA | 3,392,785 | G→A | T1158T (ACC→ACT) | yhdP ← | AsmA2 domain‑containing protein |
RA | 3,548,840 | G→A | Q411* (CAG→TAG) | malQ ← | 4‑alpha‑glucanotransferase |
RA | 3,559,459 | T→C | L398L (TTG→CTG) | rtcR → | DNA‑binding transcriptional activator RtcR |
RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
RA | 3,638,124 | T→C | V161V (GTT→GTC) | pitA → | metal phosphate:H(+) symporter PitA |
RA | 3,646,029 | T→C | G215G (GGT→GGC) | rlmJ → | 23S rRNA m(6)A2030 methyltransferase |
RA | 3,709,561 | (C)6→5 | coding (915/1692 nt) | eptB ← | Kdo2‑lipid A phosphoethanolamine 7''‑transferase |
RA | 3,760,846 | G→A | A135V (GCG→GTG) | selA ← | selenocysteine synthase |
RA | 3,765,305 | A→G | R1041R (AGA→AGG) | rhsA → | rhs element protein RhsA |
RA | 3,765,307 | C→G | T1042S (ACC→AGC) | rhsA → | rhs element protein RhsA |
RA | 3,803,350 | G→A | S263L (TCA→TTA) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
RA | 3,806,651 | T→C | K139K (AAA→AAG) | waaG ← | lipopolysaccharide glucosyltransferase I |
RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
RA | 3,820,592 | (C)6→7 | coding (579/1683 nt) | ligB ← | DNA ligase B |
RA | 3,843,478 | (C)5→4 | coding (312/1335 nt) | adeQ ← | adenine transporter |
RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
RA | 3,954,748 | T→C | V424A (GTG→GCG) | ilvD → | dihydroxy‑acid dehydratase |
RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
RA | 4,017,388 | G→A | G19D (GGC→GAC) | rmuC → | putative recombination limiting protein RmuC |
RA | 4,101,899 | A→G | V70V (GTA→GTG) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
RA | 4,112,221 | T→C | intergenic (‑7/‑94) | yiiQ ← / → yiiR | DUF1454 domain‑containing protein YiiQ/DUF805 domain‑containing protein YiiR |
RA | 4,145,150 | A→G | T386A (ACC→GCC) | pflD → | putative formate acetyltransferase 2 |
RA | 4,286,402 | C→T | G324S (GGT→AGT) | 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 | 4,306,202 | A→G | D132D (GAT→GAC) | yjcS ← | alkyl sulfatase |
RA | 4,310,124 | A→G | V286A (GTC→GCC) | alsA ← | D‑allose ABC transporter ATP binding subunit |
RA | 4,356,143 | A→G | V90A (GTG→GCG) | dtpC ← | dipeptide/tripeptide:H(+) symporter DtpC |
JC | 4,357,864 | (TCA)4→3 | coding (752‑754/2148 nt) | cadA ← | lysine decarboxylase 1 |
RA | 4,385,931 | (A)7→6 | coding (228/315 nt) | yjeO → | conserved inner membrane protein YjeO |
RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
RA | 4,458,745 | (G)5→4 | coding (787/1353 nt) | pmbA → | metalloprotease PmbA |
RA | 4,510,483 | T→C | intergenic (+350/+207) | yjhV → / ← fecE | KpLE2 phage‑like element; putative uncharacterized protein YjhV/ferric citrate ABC transporter ATP binding subunit |
RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
RA | 4,615,987 | A→G | V360A (GTC→GCC) | yjjI ← | DUF3029 domain‑containing protein YjjI |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 1433778–1434070 | 1434220–1434074 | 5–443 | 24 [23] | [21] 24 | [ynaE] | [ynaE] |
* | * | ÷ | NC_000913 | 3423785–3424234 | 3424523–3424238 | 5–739 | 26 [20] | [13] 26 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 1207790 = | 5 (0.060) | 109 (1.430) | 61/244 | 0.1 | 91.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | 1209619 = | 15 (0.200) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1207805 | 5 (0.060) | 47 (0.620) | 38/244 | 0.7 | 82.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
? | NC_000913 | = 1209602 | 15 (0.200) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 94 (1.120) | 58/268 | 0.2 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
* | ? | NC_000913 | 3363001 = | 122 (1.410) | 120 (1.400) | 59/274 | 0.2 | 65.9% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
? | NC_000913 | 3766087 = | 3 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
* | ? | NC_000913 | = 3653230 | NA (NA) | 114 (1.320) | 70/276 | 0.1 | 96.6% | noncoding (1/1195 nt) | IS5 | repeat region |
? | NC_000913 | = 3766089 | 4 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA |