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 | 37,546 | G→T | 5.4% | N93K (AAC→AAA) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| RA | 57,829 | G→T | 7.8% | V156F (GTC→TTC) | djlA → | membrane‑anchored DnaK co‑chaperone, DNA‑binding protein |
| RA | 88,279 | G→A | 9.1% | R127H (CGC→CAC) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3) |
| RA | 180,546 | G→T | 12.8% | P13T (CCT→ACT) | yaeH ← | UPF0325 family protein |
| RA | 188,645 | G→A | 5.5% | A102T (GCT→ACT) | pyrH → | uridylate kinase |
| RA | 199,599 | G→T | 5.0% | V185F (GTC→TTC) | lpxA → | UDP‑N‑acetylglucosamine acetyltransferase |
| RA | 221,373:1 | +G | 7.4% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 7.8% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 7.8% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 7.9% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 8.1% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 8.1% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 8.1% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 8.1% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 8.5% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 9.1% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 9.2% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 9.9% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 12.6% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 13.2% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 15.0% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 13.9% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 14.7% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 16.4% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 243,980 | G→A | 11.1% | intergenic (+32/‑144) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,984 | Δ1 bp | 11.1% | intergenic (+36/‑140) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,985 | A→G | 10.4% | intergenic (+37/‑139) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,986 | C→T | 10.4% | intergenic (+38/‑138) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,989:1 | +T | 10.4% | intergenic (+41/‑135) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 243,991 | G→A | 10.5% | intergenic (+43/‑133) | yafL → / → rayT | putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase; TnpA(REP) |
| RA | 249,908 | A→G | 6.3% | intergenic (+260/‑58) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 249,918 | T→A | 7.5% | intergenic (+270/‑48) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 249,924 | T→C | 7.5% | intergenic (+276/‑42) | yafP → / → ykfJ | putative acyl‑CoA transferase/pseudogene |
| RA | 267,750 | A→G | 6.1% | pseudogene (276/426 nt) | insN → | pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 310,305 | G→T | 7.3% | pseudogene (238/872 nt) | eaeH → | pseudogene, attaching and effacing protein homology;factor; Not classified |
| RA | 317,988 | G→T | 8.0% | G224W (GGG→TGG) | ykgE → | cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component |
| RA | 353,568 | G→A | 8.3% | A278A (GCC→GCT) | cynR ← | transcriptional activator of cyn operon; autorepressor |
| RA | 413,527 | C→T | 6.3% | R61R (CGC→CGT) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 416,138 | G→A | 6.0% | W364* (TGG→TGA) | brnQ → | branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val |
| RA | 457,911 | G→T | 8.3% | D181Y (GAC→TAC) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 466,895 | G→T | 5.9% | L268F (TTG→TTT) | mdlB → | putative multidrug transporter subunit of ABC superfamily, ATP‑binding component |
| RA | 514,077 | G→A | 6.6% | L177L (CTG→TTG) | ybbO ← | putative oxidoreductase |
| RA | 517,788 | C→A | 7.4% | F639L (TTC→TTA) | ybbP → | putative ABC transporter permease |
| RA | 529,010 | A→G | 6.7% | T182A (ACG→GCG) | allR → | transcriptional repressor of all and gcl operons; glyoxylate‑induced |
| RA | 660,760 | G→T | 9.5% | P337Q (CCA→CAA) | mrdB ← | cell wall shape‑determining protein |
| RA | 687,137 | Δ1 bp | 11.8% | coding (104/879 nt) | ybeX ← | putative ion transport |
| RA | 687,138 | C→A | 11.8% | D35Y (GAC→TAC) | ybeX ← | putative ion transport |
| RA | 687,139 | A→G | 11.8% | R34R (CGT→CGC) ‡ | ybeX ← | putative ion transport |
| RA | 687,141 | G→C | 11.8% | R34G (CGT→GGT) ‡ | ybeX ← | putative ion transport |
| RA | 727,315 | T→C | 5.3% | H759H (CAT→CAC) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,501 | C→A | 5.7% | H821Q (CAC→CAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,138 | A→G | 5.4% | pseudogene (550/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 733,913 | T→C | 5.5% | R122R (CGT→CGC) | ybfD → | H repeat‑associated putative transposase |
| RA | 733,915 | A→G | 5.8% | K123R (AAG→AGG) | ybfD → | H repeat‑associated putative transposase |
| RA | 733,986 | A→G | 9.8% | K147E (AAG→GAG) | ybfD → | H repeat‑associated putative transposase |
| RA | 750,710:1 | +T | 5.3% | coding (78/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 750,710:2 | +C | 5.3% | coding (78/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 750,710:3 | +C | 5.3% | coding (78/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 750,710:4 | +A | 5.3% | coding (78/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 750,710:5 | +T | 5.3% | coding (78/390 nt) | sdhC → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 776,297:1 | +T | 6.3% | intergenic (+1/‑2) | valT → / → lysW | tRNA‑Val/tRNA‑Lys |
| RA | 776,297:2 | +T | 6.3% | intergenic (+1/‑2) | valT → / → lysW | tRNA‑Val/tRNA‑Lys |
| RA | 782,865 | C→T | 7.5% | A63T (GCT→ACT) | gpmA ← | phosphoglyceromutase 1 |
| RA | 860,523 | A→G | 6.1% | F21F (TTT→TTC) | moeB ← | molybdopterin synthase sulfurylase |
| RA | 906,069 | C→A | 6.4% | R146L (CGC→CTC) | poxB ← | pyruvate dehydrogenase (pyruvate oxidase), thiamine triphosphate‑binding, FAD‑binding |
| RA | 1,004,495 | T→C | 6.9% | L399P (CTG→CCG) | rlmL → | fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent |
| RA | 1,005,220 | G→T | 14.3% | D641Y (GAT→TAT) | rlmL → | fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent |
| RA | 1,017,266 | A→C | 9.2% | L692V (TTG→GTG) | yccS ← | putative transporter, FUSC superfamily inner membrane protein, tandem domains |
| RA | 1,031,489 | C→A | 5.3% | L88L (CTC→CTA) | hyaD → | hydrogenase 1 maturation protease |
| RA | 1,042,670 | G→T | 10.5% | N244K (AAC→AAA) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,083,974 | C→T | 5.9% | G447D (GGC→GAC) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,112,491 | G→T | 11.4% | E77* (GAA→TAA) | yceA → | putative rhodanese‑related sulfurtransferase |
| RA | 1,143,276 | C→A | 5.4% | S67* (TCA→TAA) | plsX → | putative phosphate acyltransferase |
| RA | 1,158,992 | C→A | 5.7% | P93T (CCC→ACC) | thiK → | thiamine kinase |
| RA | 1,159,243 | G→A | 5.7% | V176V (GTG→GTA) | thiK → | thiamine kinase |
| RA | 1,161,906 | G→T | 7.0% | L122L (CTG→CTT) | ndh → | respiratory NADH dehydrogenase 2/cupric reductase |
| RA | 1,201,088 | G→T | 10.4% | P28P (CCG→CCT) | ymfR → | e14 prophage; uncharacterized protein |
| RA | 1,265,505 | A→G | 5.2% | intergenic (+126/+189) | rdlB → / ← ldrC | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB/toxic polypeptide, small |
| RA | 1,282,249 | A→G | 9.0% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,599 | G→A | 5.5% | noncoding (94/171 nt) P12S (CCA→TCA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,282,617 | G→A | 6.5% | noncoding (76/171 nt) Q6* (CAA→TAA) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,344,391 | C→A | 10.5% | intergenic (‑27/+117) | yciW ← / ← fabI | putative oxidoreductase/enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent |
| RA | 1,356,013:1 | +A | 5.4% | coding (637/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,356,013:2 | +C | 5.4% | coding (637/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,356,013:3 | +G | 5.4% | coding (637/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,356,015:1 | +A | 5.3% | coding (639/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,356,015:2 | +A | 5.3% | coding (639/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,356,020:1 | +C | 5.4% | coding (644/765 nt) | puuD → | gamma‑glutamyl‑gamma‑aminobutyrate hydrolase |
| RA | 1,380,170 | G→T | 5.4% | E135* (GAA→TAA) | ycjF → | UPF0283 family inner membrane protein |
| RA | 1,422,798 | A→G | 6.3% | pseudogene (186/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,456,418 | G→C | 9.3% | A13P (GCG→CCG) ‡ | paaK → | phenylacetyl‑CoA ligase |
| RA | 1,456,419 | C→T | 9.2% | A13V (GCG→GTG) ‡ | paaK → | phenylacetyl‑CoA ligase |
| RA | 1,456,424 | G→C | 9.5% | V15L (GTT→CTT) | paaK → | phenylacetyl‑CoA ligase |
| RA | 1,549,494 | G→T | 5.5% | H145N (CAT→AAT) | maeA ← | malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme) |
| RA | 1,564,221 | C→T | 8.9% | A176T (GCT→ACT) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,603,806 | C→A | 9.5% | G378W (GGG→TGG) | uxaB ← | altronate oxidoreductase, NAD‑dependent |
| RA | 1,643,276 | G→T | 8.2% | R66I (AGA→ATA) | ydfC → | uncharacterized protein, Qin prophage |
| RA | 1,662,148 | C→A | 9.5% | G225V (GGG→GTG) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| RA | 1,665,689 | C→A | 8.9% | A19A (GCC→GCA) | asr → | acid shock‑inducible periplasmic protein |
| RA | 1,665,696 | G→A | 8.5% | A22T (GCA→ACA) | asr → | acid shock‑inducible periplasmic protein |
| RA | 1,753,545 | C→A | 6.7% | M1M (ATG→ATT) † | sufE ← | sulfur acceptor protein |
| RA | 1,812,721 | C→A | 14.3% | G13W (GGG→TGG) | chbF ← | phospho‑chitobiase; general 6‑phospho‑beta‑glucosidase activity |
| RA | 1,837,699 | C→T | 7.8% | L358L (CTG→TTG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,854,801 | G→T | 8.0% | A263A (GCC→GCA) | ydjL ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,861,249 | C→A | 12.7% | R29R (CGG→AGG) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,879,434 | G→T | 9.5% | L171L (CTG→CTT) | yeaW → | putative YeaWX dioxygenase alpha subunit; 2Fe‑2S cluster |
| RA | 1,885,228 | C→T | 5.6% | A99A (GCG→GCA) | tsaB ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein; binding partner and protease for TsaD |
| RA | 1,988,643 | C→T | 6.8% | T66T (ACG→ACA) | uvrY ← | response regulator in two‑component regulatory system with BarA |
| RA | 1,993,129 | C→A | 10.0% | M246I (ATG→ATT) | fliY ← | cystine transporter subunit |
| RA | 2,051,854 | G→T | 11.4% | L440M (CTG→ATG) | yeeO ← | putative multdrug exporter, MATE family |
| RA | 2,057,156 | C→A | 9.5% | G265* (GGA→TGA) | cobT ← | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,109,590 | G→T | 12.1% | P340Q (CCG→CAG) | wcaL ← | putative glycosyl transferase |
| RA | 2,248,518 | C→A | 6.0% | G50C (GGC→TGC) | rihB ← | ribonucleoside hydrolase 2 |
| RA | 2,255,258 | C→T | 7.7% | G196D (GGC→GAC) | fruK ← | fructose‑1‑phosphate kinase |
| RA | 2,269,463 | G→T | 7.6% | A238S (GCA→TCA) | yejE → | microcin C transporter YejABEF, permease subunit; ABC family |
| RA | 2,272,135 | C→T | 7.0% | A369T (GCA→ACA) | bcr ← | bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,298,128 | C→T | 7.6% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,334,140 | C→T | 17.4% | R1170H (CGT→CAT) | yfaL ← | adhesin |
| RA | 2,337,087 | T→C | 6.9% | I188V (ATT→GTT) | yfaL ← | adhesin |
| RA | 2,367,214 | G→A | 8.2% | R423R (CGC→CGT) | menE ← | O‑succinylbenzoate‑CoA ligase |
| RA | 2,372,091 | G→T | 6.5% | F216L (TTC→TTA) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,399,955 | C→A | 100% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,459,350 | G→T | 8.7% | A191S (GCG→TCG) | yfdC → | putative inner membrane protein |
| RA | 2,465,493 | G→A | 5.7% | pseudogene (109/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,465,527 | C→T | 5.1% | pseudogene (75/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,483,208 | G→T | 8.9% | S153Y (TCT→TAT) | yfdV ← | putative transporter |
| RA | 2,517,964 | G→T | 5.7% | R92S (CGT→AGT) | xapA ← | purine nucleoside phosphorylase II |
| RA | 2,520,682 | C→A | 7.2% | V126V (GTC→GTA) | yfeH → | putative inorganic ion transporter |
| RA | 2,528,643 | G→A | 5.8% | E407K (GAA→AAA) | ptsI → | PEP‑protein phosphotransferase of PTS system (enzyme I) |
| RA | 2,546,828 | C→T | 7.7% | A82V (GCC→GTC) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,583,527 | G→T | 6.3% | T858T (ACG→ACT) | acrD → | aminoglycoside/multidrug efflux system |
| RA | 2,700,215 | C→A | 7.9% | R90L (CGT→CTT) | lepA ← | back‑translocating elongation factor EF4, GTPase |
| RA | 2,710,839 | C→A | 8.0% | intergenic (+37/+11) | ung → / ← yfiF | uracil‑DNA‑glycosylase/putative methyltransferase |
| RA | 2,719,426 | T→C | 11.4% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,767,582 | G→T | 30.8% | M302I (ATG→ATT) | yfjW → | CP4‑57 prophage; putative inner membrane protein |
| RA | 2,770,182 | T→C | 6.8% | V146V (GTT→GTC) | yfjY → | CP4‑57 prophage; putative DNA repair protein |
| RA | 2,797,662 | G→T | 10.7% | E268* (GAA→TAA) | nrdF → | ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like protein |
| RA | 2,857,477 | G→T | 6.5% | E176* (GAA→TAA) | ygbL → | putative class II aldolase |
| RA | 2,859,886 | G→T | 10.5% | intergenic (+62/+32) | ygbN → / ← rpoS | putative transporter/RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,878,987 | G→T | 10.3% | P531Q (CCA→CAA) | ygcB ← | R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity |
| RA | 2,913,916 | G→T | 7.7% | L64I (CTT→ATT) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 2,916,019 | C→A | 7.9% | A109S (GCC→TCC) | yqcA ← | short‑chain flavodoxin, FMN‑binding |
| RA | 2,916,581 | C→T | 6.3% | R188H (CGC→CAC) | truC ← | tRNA(Ile1,Asp) pseudouridine(65) synthase |
| RA | 2,946,702 | C→A | 7.0% | E887D (GAG→GAT) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 2,974,578 | C→A | 5.0% | G322W (GGG→TGG) | araE ← | arabinose transporter |
| RA | 2,994,615 | C→A | 13.8% | N304K (AAC→AAA) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,005,339 | G→A | 9.2% | V174I (GTT→ATT) | yqeA → | putative amino acid kinase |
| RA | 3,039,179 | C→A | 6.2% | V28L (GTG→TTG) | ygfF ← | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 3,070,278 | G→T | 5.1% | L180M (CTG→ATG) | yggP ← | putative Zn‑binding dehydrogenase |
| RA | 3,079,560 | G→T | 6.0% | S5S (TCG→TCT) | yqgC → | uncharacterized protein |
| RA | 3,101,555 | C→A | 5.6% | P320P (CCG→CCT) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,157,219 | C→A | 13.6% | R705L (CGC→CTC) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,158,918 | C→A | 8.0% | G139W (GGG→TGG) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,216,158 | C→A | 6.8% | P56Q (CCG→CAG) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,227,896 | G→T | 6.8% | intergenic (‑82/+202) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,281,121 | G→T | 7.6% | A113S (GCA→TCA) | yraH → | putative fimbrial‑like adhesin protein |
| RA | 3,287,986 | C→T | 5.1% | P410S (CCG→TCG) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,352,534 | A→G | 8.4% | Q1484R (CAG→CGG) | gltB → | glutamate synthase, large subunit |
| RA | 3,386,919 | G→A | 8.0% | A900V (GCG→GTG) | yhdP ← | DUF3971‑AsmA2 domains protein |
| RA | 3,395,713 | G→T | 5.9% | Q327K (CAG→AAG) | csrD ← | targeting factor for csrBC sRNA degradation |
| RA | 3,400,705 | C→T | 5.2% | intergenic (+80/‑29) | accC → / → yhdT | acetyl‑CoA carboxylase, biotin carboxylase subunit/DUF997 family putative inner membrane protein |
| RA | 3,416,890 | T→G | 12.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 19.4% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,417,055 | G→A | 7.7% | noncoding (92/120 nt) | rrfD ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,474,319 | G→T | 5.5% | Q68K (CAG→AAG) | kefG ← | potassium‑efflux system ancillary protein for KefB, glutathione‑regulated |
| RA | 3,492,008 | C→T | 8.0% | Y274Y (TAC→TAT) | cysG → | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| RA | 3,503,871 | G→T | 6.8% | D155E (GAC→GAA) | yhfX ← | putative pyridoxal 5'‑phosphate binding protein |
| RA | 3,517,154 | G→T | 5.7% | D309Y (GAC→TAC) | mrcA → | fused penicillin‑binding protein 1a: murein transglycosylase/murein transpeptidase |
| RA | 3,519,092 | G→T | 6.6% | G139G (GGC→GGA) | nudE ← | adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH |
| RA | 3,551,254 | G→T | 6.2% | P62Q (CCG→CAG) | rtcB ← | RNA‑splicing ligase |
| RA | 3,570,866 | C→T | 8.2% | A29A (GCG→GCA) | gntK ← | gluconate kinase 2 |
| RA | 3,571,475 | C→A | 6.2% | A204A (GCG→GCT) | gntR ← | d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,587,570 | T→C | 7.0% | Q424R (CAG→CGG) | livM ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,679,048 | C→A | 8.4% | intergenic (‑70/+12) | yhjK ← / ← bcsC | cyclic‑di‑GMP phosphodiesterase/cellulose synthase subunit |
| RA | 3,679,536 | T→C | 6.0% | T1000A (ACA→GCA) | bcsC ← | cellulose synthase subunit |
| RA | 3,687,976 | C→A | 5.4% | L207L (CTG→CTT) | bcsA ← | cellulose synthase, catalytic subunit |
| RA | 3,776,312 | G→T | 5.2% | P237H (CCT→CAT) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| RA | 3,893,935 | C→A | 7.0% | M1M (ATG→ATT) † | yieL ← | putative xylanase |
| RA | 3,897,509 | C→T | 8.7% | M483I (ATG→ATA) | bglF ← | fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 3,940,567 | G→T | 10.6% | A254D (GCC→GAC) | hdfR ← | flhDC operon transcriptional repressor |
| RA | 3,944,464 | C→A | 5.6% | pseudogene (545/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,961,358 | C→A | 8.4% | A28E (GCA→GAA) | wecA → | UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| RA | 3,967,277 | C→A | 12.3% | L104M (CTG→ATG) | rffH → | glucose‑1‑phosphate thymidylyltransferase |
| RA | 4,016,984 | C→T | 5.8% | A24V (GCT→GTT) | tatD → | quality control of Tat‑exported FeS proteins; Mg‑dependent cytoplasmic DNase |
| RA | 4,045,150 | C→A | 6.2% | D148E (GAC→GAA) | yihI → | activator of Der GTPase |
| RA | 4,061,147 | C→A | 6.3% | G497V (GGA→GTA) | yihQ ← | alpha‑glucosidase |
| RA | 4,073,371 | G→T | 6.5% | intergenic (+42/+288) | yiiF → / ← fdhE | putative thymol sensitivity protein, CopG family putative transcriptional regulator/formate dehydrogenase formation protein |
| RA | 4,081,584 | C→A | 12.5% | A544A (GCG→GCT) | frvR ← | putative frv operon regulator; contains a PTS EIIA domain |
| RA | 4,134,720 | G→C | 5.1% | S266S (TCG→TCC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,142,121 | C→A | 9.7% | L302L (CTG→CTT) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,142,122:1 | +T | 8.7% | coding (905/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,142,122:2 | +T | 8.7% | coding (905/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,142,122:3 | +C | 8.7% | coding (905/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,142,122:4 | +T | 8.7% | coding (905/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,142,122:5 | +C | 8.7% | coding (905/2652 nt) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,165,886 | G→A | 5.4% | K5K (AAG→AAA) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,176,469 | A→G | 93.9% | K398E (AAG→GAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 17.1% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,199,631 | T→A | 5.5% | intergenic (+15/‑71) | rrsE → / → gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu |
| RA | 4,199,637 | C→A | 5.2% | intergenic (+21/‑65) | rrsE → / → gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu |
| RA | 4,262,332 | C→T | 7.5% | G490S (GGT→AGT) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,267,596 | G→T | 10.3% | G67V (GGC→GTC) | soxR → | redox‑sensitive transcriptional activator of soxS; autorepressor |
| RA | 4,278,408 | G→A | 7.1% | E239E (GAG→GAA) | nrfA → | nitrite reductase, formate‑dependent, cytochrome |
| RA | 4,325,829 | G→T | 6.0% | S340R (AGC→AGA) | adiC ← | arginine:agmatine antiporter |
| RA | 4,327,091 | G→T | 13.1% | S219Y (TCC→TAC) | adiY ← | adi system transcriptional activator |
| RA | 4,329,208 | G→T | 5.0% | T377T (ACC→ACA) | adiA ← | arginine decarboxylase |
| RA | 4,336,187 | G→A | 7.1% | S319S (TCC→TCT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,376,690 | G→A | 8.7% | A833V (GCG→GTG) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,412,401 | G→A | 5.7% | V133V (GTG→GTA) | ulaD → | 3‑keto‑L‑gulonate 6‑phosphate decarboxylase |
| RA | 4,434,541 | G→T | 5.4% | E205* (GAA→TAA) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,468,243 | G→T | 7.3% | intergenic (‑115/‑47) | argI ← / → rraB | ornithine carbamoyltransferase 1/protein inhibitor of RNase E |
| RA | 4,549,855 | A→G | 8.2% | F215L (TTC→CTC) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| RA | 4,587,866 | C→T | 10.3% | E465K (GAA→AAA) | opgB ← | phosphoglycerol transferases I and II |
| RA | 4,594,850 | G→T | 5.1% | R211S (CGC→AGC) | fhuF ← | ferric iron reductase involved in ferric hydroximate transport |
| RA | 4,608,466 | C→A | 10.3% | R141S (CGT→AGT) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1459366 | 1459554 | 189 | 8 [7] | [7] 8 | ynbG | ynbG |
| * | * | ÷ | CP009273 | 1524311 | 1524429 | 119 | 9 [6] | [7] 8 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 2208322 | 2209078 | 757 | 8 [7] | [6] 13 | mlrA | mlrA |
| * | * | ÷ | CP009273 | 2988469 | 2988682 | 214 | 9 [7] | [7] 9 | [ygeN] | [ygeN] |
| * | * | ÷ | CP009273 | 3448766 | 3448865 | 100 | 11 [5] | [0] 10 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 56 (1.000) | 53 (0.950) | 30/250 | NT | 48.6% | 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 | = 367021 | 0 (0.000) | 3 (0.050) | 3/250 | NT | 100% | noncoding (1031/1223 nt) | IS30 | repeat region |
| ? | CP009273 | 367026 = | NA (NA) | noncoding (1036/1223 nt) | IS30 | repeat region | |||||
| * | ? | CP009273 | 370704 = | 72 (1.290) | 8 (0.170) | 4/212 | NT | 11.4% | noncoding (319/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372963 = | 63 (1.330) | noncoding (173/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 1203246 = | 28 (0.500) | 25 (0.510) | 17/218 | NT | 60.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 9 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 26 (0.460) | 28 (0.570) | 12/218 | NT | 63.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 9 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1972769 = | 28 (0.500) | 5 (0.090) | 4/248 | NT | 15.3% | intergenic (‑315/‑465) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | 2282498 = | NA (NA) | 3 (0.050) | 3/248 | NT | 7.4% | noncoding (1095/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2340666 | 38 (0.680) | noncoding (28/203 nt) | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences | REP164 (repetitive extragenic palindromic) element; contains 5 REP sequences | |||||
| * | ? | CP009273 | = 2283592 | NA (NA) | 8 (0.150) | 3/246 | NT | 12.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2399636 = | 54 (0.980) | coding (485/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes | |||||