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 | freq | annotation | gene | description |
| RA | 576 | C→A | 5.7% | A80A (GCC→GCA) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 7,238 | G→A | 5.1% | A241V (GCT→GTT) | yaaJ ← | putative transporter |
| RA | 39,017 | G→T | 6.1% | F33L (TTC→TTA) | caiB ← | crotonobetainyl CoA:carnitine CoA transferase |
| RA | 138,073 | G→T | 6.3% | L52L (CTG→CTT) | hpt → | hypoxanthine phosphoribosyltransferase |
| RA | 148,367 | C→A | 5.5% | G118C (GGT→TGT) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 155,747 | C→T | 6.1% | V285I (GTC→ATC) | gluQ ← | glutamyl‑Q tRNA(Asp) synthetase |
| RA | 221,425 | T→C | 6.8% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 7.0% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 222,173 | T→C | 6.1% | intergenic (+111/‑73) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA of rrnH operon |
| RA | 262,393 | C→T | 6.0% | pseudogene (93/222 nt) | ykfL ← | pseudogene, CP4‑6 putative prophage remnant;Phage or Prophage Related |
| RA | 263,324 | A→G | 6.7% | G131G (GGT→GGC) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,333 | G→C | 6.7% | L128L (CTC→CTG) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 263,336 | C→A | 7.5% | G127G (GGG→GGT) | yafZ ← | CP4‑6 prophage; conserved protein |
| RA | 274,938 | T→A | 11.4% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 290,327 | G→T | 6.0% | H62N (CAC→AAC) | yagM ← | CP4‑6 prophage; uncharacterized protein |
| RA | 297,505 | T→C | 6.1% | T32A (ACC→GCC) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 297,542 | A→G | 6.0% | A19A (GCT→GCC) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 342,623 | G→T | 6.6% | A511E (GCG→GAG) | prpR ← | propionate catabolism operon regulatory protein |
| RA | 350,138 | C→T | 5.9% | G574G (GGC→GGT) | prpE → | propionate‑‑CoA ligase |
| RA | 356,856 | G→T | 5.2% | *385L (TGA→TTA) | cynX → | putative cyanate transporter |
| RA | 415,386 | Δ1 bp | 5.6% | coding (340/1320 nt) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 418,995 | T→G | 12.7% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 506,620 | C→A | 5.9% | P72P (CCG→CCT) | copA ← | copper transporter |
| RA | 519,269 | A→C | 5.7% | I185L (ATA→CTA) ‡ | rhsD → | Rhs family putative polymorphic toxin |
| RA | 519,271 | A→G | 5.7% | I185M (ATA→ATG) ‡ | rhsD → | Rhs family putative polymorphic toxin |
| RA | 519,274 | G→C | 5.8% | L186L (CTG→CTC) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 519,282 | C→G | 9.0% | S189C (TCT→TGT) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 526,984 | G→T | 5.4% | H232N (CAT→AAT) | allS ← | allD operon transcriptional activator |
| RA | 587,971 | C→A | 5.9% | D222Y (GAT→TAT) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 654,655 | C→T | 8.0% | intergenic (+49/+52) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 682,757 | G→A | 5.6% | A149A (GCC→GCT) | gltI ← | glutamate, aspartate binding protein, periplasmic; part of GltJKLI ABC transporter |
| RA | 726,100 | A→G | 9.0% | R354R (CGA→CGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 726,110 | T→C | 10.1% | C358R (TGT→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,171 | T→G | 7.0% | N711K (AAT→AAG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,174 | C→T | 6.7% | G712G (GGC→GGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,207 | C→T | 6.4% | R723R (CGC→CGT) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 8.5% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,212 | G→A | 7.0% | R1058R (AGG→AGA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 728,560 | T→C | 5.1% | G1174G (GGT→GGC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 776,297:1 | +T | 5.0% | intergenic (+1/‑2) | valT → / → lysW | tRNA‑Val/tRNA‑Lys |
| RA | 811,084 | A→T | 15.8% | intergenic (+81/+111) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 811,100 | G→T | 7.3% | intergenic (+97/+95) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 819,131 | G→T | 6.5% | P22H (CCC→CAC) | clsB ← | cardiolipin synthase 2 |
| RA | 824,808 | C→A | 6.0% | L207F (TTG→TTT) | ybhG ← | putative membrane fusion protein (MFP) component of efflux pump, membrane anchor |
| RA | 839,598 | C→A | 6.1% | G447* (GGA→TGA) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 861,196 | C→T | 7.3% | V209I (GTA→ATA) | moeA ← | molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein |
| RA | 910,669 | A→T | 28.5% | intergenic (‑356/+139) | ybjE ← / ← aqpZ | putative transporter/aquaporin Z |
| RA | 926,796 | A→G | 5.3% | V237V (GTT→GTC) | trxB ← | thioredoxin reductase, FAD/NAD(P)‑binding |
| RA | 931,037 | G→A | 6.9% | A786A (GCG→GCA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 931,040 | A→G | 6.8% | P787P (CCA→CCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 937,807 | G→A | 22.2% | V465I (GTA→ATA) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 984,786:1 | +C | 11.1% | coding (1027/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 984,786:2 | +A | 11.1% | coding (1027/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 984,786:3 | +G | 11.1% | coding (1027/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 984,786:4 | +G | 11.1% | coding (1027/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 991,716 | C→G | 7.7% | V229L (GTA→CTA) | ssuA ← | aliphatic sulfonate binding protein, SsuABC ABC transporter |
| RA | 1,045,283 | T→G | 10.3% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,091,663 | C→A | 6.3% | A122E (GCG→GAG) | ycdU → | putative inner membrane protein |
| RA | 1,126,333 | C→T | 7.5% | intergenic (‑14/‑141) | flgA ← / → flgB | assembly protein for flagellar basal‑body periplasmic P ring/flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,145,242 | C→A | 9.5% | A20D (GCT→GAT) | fabD → | malonyl‑CoA‑[acyl‑carrier‑protein] transacylase |
| RA | 1,159,361 | G→T | 6.1% | D216Y (GAC→TAC) | thiK → | thiamine kinase |
| RA | 1,181,824 | G→T | 7.3% | V175V (GTG→GTT) | pepT → | peptidase T |
| RA | 1,203,115 | A→C | 5.3% | A53A (GCA→GCC) | stfP → | e14 prophage; uncharacterized protein |
| RA | 1,218,978 | C→T | 6.9% | intergenic (+73/‑42) | ymgJ → / → ycgI | uncharacterized protein/pseudogene |
| RA | 1,223,830 | C→A | 5.9% | A99E (GCG→GAG) | ycgM → | putative isomerase/hydrolase |
| RA | 1,259,176 | C→T | 5.7% | L3F (CTT→TTT) | hemA → | glutamyl tRNA reductase |
| RA | 1,264,647 | T→C | 30.0% | S29G (AGC→GGC) | ldrA ← | toxic polypeptide, small |
| RA | 1,264,818 | G→T | 9.2% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| RA | 1,265,888 | T→G | 5.7% | noncoding (40/68 nt) | rdlC → | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC |
| RA | 1,266,001 | G→T | 8.2% | intergenic (+85/+204) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,279,542 | C→A | 5.3% | F161L (TTC→TTA) | narH → | nitrate reductase 1, beta (Fe‑S) subunit |
| RA | 1,282,249 | A→G | 8.6% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,497 | A→G | 6.2% | intergenic (+515/+25) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,302,861 | C→A | 5.8% | L14L (CTG→CTT) | clsA ← | cardiolipin synthase 1 |
| RA | 1,307,809 | C→A | 5.3% | G38W (GGG→TGG) | yciC ← | UPF0259 family inner membrane protein |
| RA | 1,314,784:1 | +C | 7.7% | coding (858/1596 nt) | trpD ← | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase |
| RA | 1,362,759 | C→T | 6.7% | R142C (CGT→TGT) | pspA → | regulatory protein for phage‑shock‑protein operon |
| RA | 1,422,040 | A→G | 20.3% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,060 | G→C | 21.1% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,168 | A→C | 5.0% | pseudogene (816/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,252 | A→G | 6.0% | pseudogene (732/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 5.6% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,648 | G→C | 5.5% | pseudogene (336/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,426,026 | C→T | 6.0% | G907G (GGC→GGT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,426,087 | G→A | 6.7% | A928T (GCT→ACT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,426,200 | G→A | 6.5% | L965L (TTG→TTA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,449,375 | C→A | 7.1% | T84K (ACG→AAG) | paaB → | putative ring 1,2‑phenylacetyl‑CoA epoxidase subunit |
| RA | 1,450,821 | A→G | 5.2% | K45K (AAA→AAG) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| RA | 1,460,602 | T→C | 5.9% | pseudogene (954/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,689 | A→G | 8.1% | pseudogene (1041/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,695 | T→G | 7.3% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 5.3% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,887 | G→C | 5.1% | pseudogene (1239/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,896 | C→T | 6.8% | pseudogene (1248/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,478,291 | C→A | 10.1% | A325E (GCG→GAG) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,495,185 | A→G | 5.5% | Y119C (TAT→TGT) | tehA → | potassium‑tellurite ethidium and proflavin transporter |
| RA | 1,522,209 | C→T | 5.2% | pseudogene (51/2037 nt) | rhsE → | pseudogene, Rhs family protein |
| RA | 1,536,113 | A→G | 5.9% | Y245Y (TAT→TAC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,583,663 | T→C | 5.2% | pseudogene (674/1227 nt) | ydeT ← | pseudogene; putative outer membrane protein |
| RA | 1,628,897 | G→C | 6.2% | G82G (GGC→GGG) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,900 | G→T | 6.2% | S81S (TCC→TCA) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,903 | A→C | 6.2% | A80A (GCT→GCG) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,628,906 | C→T | 6.4% | V79V (GTG→GTA) | tfaQ ← | Qin prophage; putative tail fiber assembly protein |
| RA | 1,629,619 | G→A | 6.4% | H162H (CAC→CAT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,667,021 | C→A | 7.5% | Q269K (CAA→AAA) | ydgD → | putative peptidase |
| RA | 1,705,195 | C→A | 6.6% | N37K (AAC→AAA) | rsxE → | SoxR iron‑sulfur cluster reduction factor component; electron transport inner membrane NADH‑quinone reductase |
| RA | 1,808,054 | G→T | 6.9% | intergenic (‑134/‑70) | cedA ← / → katE | cell division modulator/catalase HPII, heme d‑containing |
| RA | 1,889,552 | G→T | 6.0% | R164L (CGG→CTG) | pabB → | aminodeoxychorismate synthase, subunit I |
| RA | 1,890,261 | C→T | 6.6% | C400C (TGC→TGT) | pabB → | aminodeoxychorismate synthase, subunit I |
| RA | 1,900,800 | C→A | 6.8% | W173L (TGG→TTG) | rlmA ← | 23S rRNA m(1)G745 methyltransferase, SAM‑dependent |
| RA | 1,910,467 | C→A | 8.1% | intergenic (‑82/‑48) | msrC ← / → yebS | free methionine‑(R)‑sulfoxide reductase/inner membrane protein |
| RA | 1,922,808:1 | +A | 12.0% | coding (289/2061 nt) | ptrB ← | protease II |
| RA | 1,934,657 | C→A | 7.9% | L412L (CTG→CTT) | mepM ← | murein DD‑endopeptidase, space‑maker hydrolase, septation protein |
| RA | 1,938,416 | T→G | 6.2% | L249R (CTG→CGG) | znuB → | zinc transporter subunit: membrane component of ABC superfamily |
| RA | 1,984,190 | G→T | 6.5% | A343A (GCG→GCT) | tyrP → | tyrosine transporter |
| RA | 1,984,666 | C→A | 5.6% | A145A (GCG→GCT) | yecA ← | UPF0149 family protein |
| RA | 2,023,321 | T→C | 7.9% | V101A (GTA→GCA) | yedA → | amino acid exporter for phenylalanine, threonine |
| RA | 2,046,345 | C→T | 6.4% | pseudogene (465/1053 nt) | yeeL ← | pseudogene, glycosyltransferase homology |
| RA | 2,053,685 | C→A | 5.7% | G237G (GGG→GGT) | cbl ← | ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,059,656 | T→C | 6.6% | intergenic (‑21/+130) | yeeH ← / ← insH1 | pseudogene/IS5 transposase and trans‑activator |
| RA | 2,170,085 | C→T | 8.2% | W200* (TGG→TAG) | gatY ← | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit |
| RA | 2,170,724 | G→T | 21.3% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,170,758 | C→A | 20.0% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,180,931 | G→T | 6.4% | Y321* (TAC→TAA) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,215,365 | T→C | 10.3% | D35G (GAT→GGT) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,219,620 | G→T | 5.1% | G114V (GGT→GTT) ‡ | yohD → | DedA family inner membrane protein |
| RA | 2,219,621 | T→C | 5.1% | G114G (GGT→GGC) ‡ | yohD → | DedA family inner membrane protein |
| RA | 2,219,622 | G→T | 5.3% | A115S (GCC→TCC) | yohD → | DedA family inner membrane protein |
| RA | 2,236,832 | G→T | 12.5% | V100V (GTC→GTA) | folE ← | GTP cyclohydrolase I |
| RA | 2,239,031 | G→T | 5.8% | D406E (GAC→GAA) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,298,241 | T→C | 8.3% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,298,492 | A→G | 6.5% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,299,172 | G→A | 5.1% | N354N (AAC→AAT) | mqo ← | malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,309,494 | G→T | 6.2% | R843L (CGT→CTT) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,325,320 | G→T | 7.9% | pseudogene (2562/4605 nt) | yfaS ← | pseudogene, bacterial alpha2‑macroglobulin YfaS variant family; putative membrane protein |
| RA | 2,331,882 | C→A | 5.6% | G340C (GGT→TGT) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,408,729 | C→T | 5.1% | T168T (ACC→ACT) | pta → | phosphate acetyltransferase |
| RA | 2,514,486 | C→A | 7.9% | intergenic (+1/‑46) | valU → / → valY | tRNA‑Val/tRNA‑Val |
| RA | 2,514,609 | Δ1 bp | 9.3% | intergenic (+2/‑3) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,566,600 | C→A | 6.4% | G89C (GGC→TGC) | eutD ← | phosphate acetyltransferase |
| RA | 2,591,127 | G→T | 5.3% | intergenic (‑150/+63) | purC ← / ← bamC | phosphoribosylaminoimidazole‑succinocarboxamide synthetase/BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,610,619 | C→A | 9.2% | G389G (GGC→GGA) | bepA → | periplasmic metalloprotease and chaperone for OM protein maintenance and assembly |
| RA | 2,664,683 | G→A | 8.1% | A34T (GCC→ACC) | hcaB → | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| RA | 2,682,911 | A→T | 5.4% | intergenic (‑46/+119) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,682,952 | T→C | 5.5% | intergenic (‑87/+78) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,682,954 | Δ1 bp | 5.6% | intergenic (‑89/+76) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,682,955 | C→A | 5.6% | intergenic (‑90/+75) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,682,964 | A→G | 5.4% | intergenic (‑99/+66) | yfhG ← / ← glrK | putative outer membrane protein modulating the QseEF response/sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,719,426 | T→C | 17.9% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,748,000 | G→T | 5.7% | Q42K (CAG→AAG) | ratA ← | toxic UPF0083 family protein inhibitor of 70S ribosome formation |
| RA | 2,762,416 | C→T | 5.1% | G131G (GGC→GGT) | yfjQ → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,776,157 | A→G | 5.7% | intergenic (‑72/+267) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| RA | 2,776,199 | A→G | 6.4% | intergenic (‑114/+225) | ypjA ← / ← pinH | adhesin‑like autotransporter/pseudogene, invertase resolvase family |
| RA | 2,801,533 | A→T | 11.5% | intergenic (+50/‑142) | proX → / → ygaY | glycine betaine transporter subunit/pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein |
| RA | 2,801,537 | T→C | 7.0% | intergenic (+54/‑138) | proX → / → ygaY | glycine betaine transporter subunit/pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein |
| RA | 2,837,487 | G→T | 5.5% | A28E (GCG→GAG) | hycG ← | hydrogenase 3 and formate hydrogenase complex, HycG subunit |
| RA | 2,898,090 | G→T | 5.4% | intergenic (+1357/+16) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,925,059 | A→G | 6.3% | K216E (AAA→GAA) | ygdG → | Ssb‑binding protein, misidentified as ExoIX |
| RA | 3,003,323 | G→A | 6.0% | A401T (GCA→ACA) | ygeY → | putative peptidase |
| RA | 3,055,270 | C→A | 6.0% | T354T (ACC→ACA) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,064,718 | T→G | 9.8% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,070,315 | C→A | 5.0% | E167D (GAG→GAT) | yggP ← | putative Zn‑binding dehydrogenase |
| RA | 3,101,778 | C→T | 5.2% | G246D (GGT→GAT) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,107,143 | G→T | 5.2% | S190Y (TCT→TAT) | pppA ← | bifunctional prepilin leader peptidase/ methylase |
| RA | 3,187,196:1 | +G | 8.1% | coding (974/1662 nt) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,196,223 | C→A | 5.1% | S325Y (TCC→TAC) | cca → | fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase |
| RA | 3,197,820 | T→C | 5.0% | K43K (AAA→AAG) | folB ← | bifunctional dihydroneopterin aldolase/dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,200,275 | G→T | 5.6% | A152S (GCA→TCA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,203,935 | T→G | 5.2% | intergenic (‑33/‑205) | tsaD ← / → rpsU | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; glycation binding protein/30S ribosomal subunit protein S21 |
| RA | 3,243,906 | G→T | 9.1% | intergenic (+171/‑15) | yqjK → / → yqjF | uncharacterized protein/putative quinol oxidase subunit |
| RA | 3,353,190 | G→T | 5.2% | E212* (GAA→TAA) | gltD → | glutamate synthase, 4Fe‑4S protein, small subunit |
| RA | 3,379,348 | C→A | 6.3% | L47L (CTG→CTT) | yhcO ← | putative barnase inhibitor |
| RA | 3,392,368 | G→T | 7.0% | Q324K (CAG→AAG) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,416,890 | T→G | 11.0% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 11.1% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,432,727 | G→T | 5.5% | R48S (CGC→AGC) | yhdN ← | DUF1992 family protein |
| RA | 3,482,330 | C→A | 6.5% | V404F (GTT→TTT) | argD ← | bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase |
| RA | 3,524,016 | T→C | 5.5% | intergenic (+5/+58) | hslO → / ← yhgE | heat shock protein Hsp33/DUF4153 family putative inner membrane protein |
| RA | 3,549,511 | C→A | 5.7% | G233V (GGT→GTT) | rtcA ← | RNA 3'‑terminal phosphate cyclase |
| RA | 3,590,084 | C→A | 10.4% | P279P (CCG→CCT) | livK ← | leucine transporter subunit |
| RA | 3,612,611 | T→C | 8.6% | V20V (GTT→GTC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,121 | G→C | 7.1% | R1190R (CGG→CGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,616,199 | A→G | 5.1% | R1216R (CGA→CGG) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,618,160 | A→G | 9.5% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,641,448 | T→C | 6.2% | noncoding (26/84 nt) | agrA → | Inactive antisense sRNA |
| RA | 3,812,401 | C→A | 5.7% | L56L (CTC→CTA) | yicG → | UPF0126 family inner membrane protein |
| RA | 3,826,590 | C→T | 6.6% | M436I (ATG→ATA) | yicI ← | putative alpha‑glucosidase |
| RA | 3,852,250 | C→A | 6.3% | Q409H (CAG→CAT) | yidK ← | putative transporter |
| RA | 3,893,994 | Δ1 bp | 5.5% | coding (1587/1617 nt) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,893,995 | G→T | 5.4% | A529D (GCT→GAT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,893,996 | C→T | 5.2% | A529T (GCT→ACT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,893,997 | A→T | 5.0% | F528L (TTT→TTA) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,893,998 | A→T | 5.0% | F528Y (TTT→TAT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,893,999 | A→T | 5.0% | F528I (TTT→ATT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,001 | Δ1 bp | 5.3% | coding (1580/1617 nt) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,002 | G→A | 5.3% | Q527* (CAG→TAG) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,003 | G→C | 5.8% | D526E (GAC→GAG) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,004 | T→C | 5.8% | D526G (GAC→GGC) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,005 | C→A | 6.0% | D526Y (GAC→TAC) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,006 | G→A | 5.8% | D525D (GAC→GAT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,008 | C→G | 5.8% | D525H (GAC→CAC) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,010 | T→A | 5.3% | K524I (AAA→ATA) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,011 | T→G | 5.7% | K524Q (AAA→CAA) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,013 | T→G | 5.9% | N523T (AAT→ACT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,014 | T→C | 5.6% | N523D (AAT→GAT) ‡ | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,894,015 | G→A | 5.7% | D522D (GAC→GAT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,935,371 | G→T | 6.7% | noncoding (204/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 3,949,200 | G→T | 5.6% | A170A (GCG→GCT) | ilvA → | L‑threonine dehydratase, biosynthetic; also known as threonine deaminase |
| RA | 4,006,613 | C→A | 13.9% | Y67* (TAC→TAA) | metE → | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 4,065,263 | A→T | 9.5% | L250Q (CTG→CAG) | yihT ← | putative aldolase |
| RA | 4,143,586 | C→T | 5.7% | intergenic (‑560/+38) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,165,449 | C→T | 20.1% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 20.3% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,178,500 | C→T | 89.2% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,195,812 | G→A | 7.3% | A16A (GCC→GCT) | purD ← | phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase |
| RA | 4,202,979 | A→C | 22.2% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,257,184 | C→T | 9.2% | A48V (GCC→GTC) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,260,762 | G→A | 5.8% | L59L (CTG→CTA) | yjbR → | DUF419 family protein |
| RA | 4,336,238 | A→G | 9.6% | R302R (CGT→CGC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,241 | G→A | 9.5% | I301I (ATC→ATT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,421,749 | C→A | 6.2% | A18S (GCT→TCT) | ytfE ← | iron‑sulfur cluster repair protein RIC |
| RA | 4,435,171 | C→A | 9.9% | Q415K (CAG→AAG) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,440,847 | G→T | 9.3% | intergenic (+112/‑28) | ytfQ → / → ytfR | galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily/putative ABC superfamily sugar transporter ATP‑binding subunit |
| RA | 4,441,770 | G→T | 12.0% | R299L (CGT→CTT) | ytfR → | putative ABC superfamily sugar transporter ATP‑binding subunit |
| RA | 4,498,944 | G→A | 6.0% | pseudogene (119/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,951 | C→A | 5.4% | pseudogene (126/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,505,305 | A→T | 5.6% | L397Q (CTG→CAG) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,508,826 | G→A | 9.6% | pseudogene (289/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,830 | A→G | 9.5% | pseudogene (293/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,885 | T→A | 5.2% | pseudogene (348/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,519,008 | C→G | 5.9% | R351S (AGG→AGC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,530,419 | C→T | 7.0% | intergenic (‑1101/‑355) | nanC ← / → fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,575,785 | A→T | 8.8% | pseudogene (848/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| RA | 4,618,118 | C→T | 5.3% | F329F (TTC→TTT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 335717 | 43 (0.520) | 11 (0.170) +29 bp |
4/188 | NT | 24.9% | noncoding (250/358 nt) | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | CP009273 | = 372985 | NA (NA) | intergenic (+218/+6) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 360104 = | 47 (0.570) | 67 (0.810) | 27/248 | NT | 58.8% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 370385 | 108 (1.790) | 28 (0.520) | 9/162 | NT | 22.4% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 370386 = | NA (NA) | 8 (0.150) | 5/162 | NT | 9.5% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372978 = | 85 (1.410) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 370704 = | 79 (0.950) | 18 (0.260) | 7/210 | NT | 18.9% | noncoding (319/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372963 = | 88 (1.250) | noncoding (173/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 1203246 = | 16 (0.190) | 49 (0.680) | 27/216 | NT | 78.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 13 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 16 (0.190) | 33 (0.460) | 12/216 | NT | 71.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 13 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2399639 | 139 (1.670) | 11 (0.130) | 7/248 | NT | 7.3% | coding (482/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes |
| ? | CP009273 | = 3124699 | NA (NA) | intergenic (+146/+1) | insH1/yghQ | IS5 transposase and trans‑activator/putative inner membrane polysaccharide flippase | |||||