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 | 25,404 | C→T | 7.3% | G66G (GGC→GGT) | lspA → | prolipoprotein signal peptidase (signal peptidase II) |
| RA | 28,023 | C→A | 5.7% | P244Q (CCG→CAG) | rihC → | ribonucleoside hydrolase 3 |
| RA | 32,674 | Δ1 bp | 5.3% | coding (1858/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 52,714 | C→T | 10.3% | A235T (GCG→ACG) | pdxA ← | 4‑hydroxy‑L‑threonine phosphate dehydrogenase, NAD‑dependent |
| RA | 64,460 | C→A | 6.3% | G441C (GGC→TGC) | polB ← | DNA polymerase II |
| RA | 66,334 | G→A | 7.5% | pseudogene (199/678 nt) | araD ← | pseudogene, truncated |
| RA | 86,249 | G→A | 5.1% | P43P (CCG→CCA) | mraZ → | RsmH methytransferase inhibitor |
| RA | 98,406 | C→A | 8.0% | T385T (ACC→ACA) | murC → | UDP‑N‑acetylmuramate:L‑alanine ligase |
| RA | 102,641 | G→T | 8.0% | A284S (GCA→TCA) | ftsZ → | GTP‑binding tubulin‑like cell division protein |
| RA | 114,001 | C→A | 12.2% | L12L (CTG→CTT) | ppdD ← | putative prepilin peptidase‑dependent pilin |
| RA | 137,334 | C→T | 11.4% | A127T (GCA→ACA) | gcd ← | glucose dehydrogenase |
| RA | 173,661 | C→T | 6.6% | A151T (GCA→ACA) | yadS ← | UPF0126 family inner membrane protein |
| RA | 187,357 | C→A | 14.9% | T5N (ACC→AAC) | tsf → | translation elongation factor EF‑Ts |
| RA | 194,814 | G→T | 5.4% | E134* (GAG→TAG) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| RA | 210,953 | G→A | 7.1% | R59H (CGT→CAT) | yaeQ → | PDDEXK superfamily protein |
| RA | 211,673 | G→T | 8.4% | R118S (AGG→AGT) | arfB → | alternative stalled‑ribosome rescue factor B; peptidyl‑tRNA hydrolase, ribosome‑attached |
| RA | 219,805 | Δ1 bp | 5.6% | coding (486/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,806 | Δ1 bp | 5.6% | coding (487/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,807 | Δ1 bp | 5.6% | coding (488/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,808 | Δ1 bp | 5.1% | coding (489/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,809 | Δ1 bp | 5.1% | coding (490/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,810 | Δ1 bp | 5.2% | coding (491/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 219,811 | Δ1 bp | 5.2% | coding (492/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 246,168 | G→T | 5.3% | pseudogene (390/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| RA | 250,838 | G→T | 12.0% | P456T (CCA→ACA) | pepD ← | aminoacyl‑histidine dipeptidase (peptidase D) |
| RA | 272,287 | C→A | 6.7% | L418M (CTG→ATG) | mmuP → | CP4‑6 prophage; putative S‑methylmethionine transporter |
| RA | 317,368 | G→T | 9.1% | R17I (AGA→ATA) | ykgE → | cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component |
| RA | 335,033 | C→A | 6.0% | P333Q (CCG→CAG) | yahG → | DUF1116 family protein |
| RA | 360,531 | G→T | 5.6% | intergenic (‑465/+130) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 360,577 | G→T | 5.8% | intergenic (‑511/+84) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| RA | 383,582 | G→T | 5.8% | G111V (GGG→GTG) | tauD → | taurine dioxygenase, 2‑oxoglutarate‑dependent |
| RA | 406,826 | G→A | 6.1% | S371L (TCG→TTG) | araJ ← | arabinose‑inducible putative transporter, MFS family |
| RA | 459,953 | G→T | 6.4% | W32C (TGG→TGT) | fadM → | long‑chain acyl‑CoA thioesterase III |
| RA | 488,877 | A→G | 5.7% | N444D (AAC→GAC) | dnaX → | DNA polymerase III/DNA elongation factor III, tau and gamma subunits |
| RA | 495,538 | G→T | 7.9% | intergenic (‑109/‑43) | aes ← / → gsk | acetyl esterase/inosine/guanosine kinase |
| RA | 495,933 | G→A | 5.9% | S118N (AGC→AAC) | gsk → | inosine/guanosine kinase |
| RA | 544,901 | G→A | 6.2% | L363L (CTG→CTA) | ylbE → | NO‑induced DUF1116 protein |
| RA | 550,421 | G→A | 6.6% | A119T (GCA→ACA) | cysS → | cysteinyl‑tRNA synthetase |
| RA | 573,883 | G→C | 6.3% | T107T (ACG→ACC) R34P (CGG→CCG) |
rzpD → rzoD → |
DLP12 prophage; putative murein endopeptidase DLP12 prophage; putative lipoprotein |
| RA | 607,340 | G→T | 9.3% | P204Q (CCG→CAG) | fepA ← | iron‑enterobactin outer membrane transporter |
| RA | 609,274 | C→A | 5.7% | P361H (CCC→CAC) | fes → | enterobactin/ferric enterobactin esterase |
| RA | 612,787 | C→T | 13.1% | P1059S (CCG→TCG) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 623,384 | C→A | 5.2% | Q79K (CAG→AAG) | entB → | isochorismatase |
| RA | 625,930 | A→C | 7.7% | Y194S (TAT→TCT) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 635,454 | G→T | 8.2% | P82P (CCG→CCT) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 658,982 | G→T | 5.9% | A146A (GCC→GCA) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) |
| RA | 677,686 | G→T | 13.0% | P388P (CCC→CCA) | hscC ← | Hsp70 family chaperone Hsc62, binds to RpoD and inhibits transcription |
| RA | 692,071 | C→A | 5.6% | noncoding (2/75 nt) | glnV ← | tRNA‑Gln |
| RA | 696,090 | G→T | 9.8% | H321N (CAT→AAT) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 774,222 | G→T | 5.3% | G343C (GGT→TGT) | tolB → | periplasmic protein |
| RA | 776,101 | G→A | 7.7% | intergenic (+16/‑120) | lysT → / → valT | tRNA‑Lys/tRNA‑Val |
| RA | 776,524 | G→T | 10.4% | noncoding (1/76 nt) | valZ → | tRNA‑Val |
| RA | 831,533 | G→T | 6.5% | W277L (TGG→TTG) | ybiB → | putative family 3 glycosyltransferase |
| RA | 833,105 | T→A | 12.5% | intergenic (+213/+16) | ybiC → / ← ybiJ | putative dehydrogenase/DUF1471 family putative periplasmic protein |
| RA | 833,435 | A→C | 11.7% | intergenic (‑54/+211) | ybiJ ← / ← ybiI | DUF1471 family putative periplasmic protein/DksA‑type zinc finger protein |
| RA | 838,513 | C→T | 6.1% | G242G (GGC→GGT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 870,325 | G→T | 9.4% | E631* (GAA→TAA) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 886,542 | C→A | 13.7% | P58P (CCC→CCA) | ybjC → | DUF1418 family protein |
| RA | 920,542 | G→T | 11.2% | G608V (GGG→GTG) | clpA → | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity |
| RA | 991,309 | C→A | 10.0% | G46C (GGT→TGT) | ssuD ← | alkanesulfonate monooxygenase, FMNH(2)‑dependent |
| RA | 998,012 | G→T | 9.5% | G250G (GGG→GGT) | elfG → | putative fimbrial‑like adhesin protein |
| RA | 1,047,460 | G→T | 7.1% | R53M (AGG→ATG) | ymcE → | cold shock gene |
| RA | 1,075,189 | G→T | 5.7% | S143S (TCG→TCT) | putP → | proline:sodium symporter |
| RA | 1,076,908 | C→A | 6.8% | pseudogene (97/105 nt) | efeU → | ferrous iron permease (pseudogene) |
| RA | 1,101,623 | G→T | 7.6% | V116V (GTG→GTT) | ymdB → | O‑acetyl‑ADP‑ribose deacetylase; RNase III inhibitor during cold shock; putative cardiolipin synthase C regulatory subunit |
| RA | 1,109,699 | G→T | 6.9% | intergenic (‑62/+21) | msyB ← / ← mdtG | multicopy suppressor of secY and secA/putative drug efflux system protein |
| RA | 1,136,351 | C→A | 7.0% | S288* (TCA→TAA) | flgL → | flagellar hook‑filament junction protein |
| RA | 1,139,323 | G→A | 6.2% | I167I (ATC→ATT) | rne ← | fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein |
| RA | 1,144,484 | A→G | 6.0% | A90A (GCA→GCG) | fabH → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,170,967 | C→A | 7.9% | L29I (CTT→ATT) ‡ | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,968 | T→C | 7.8% | L29P (CTT→CCT) ‡ | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,969 | T→A | 7.4% | L29L (CTT→CTA) ‡ | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,971 | Δ1 bp | 7.7% | coding (89/1200 nt) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,973 | Δ1 bp | 7.5% | coding (91/1200 nt) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,974 | Δ1 bp | 7.5% | coding (92/1200 nt) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,170,976 | A→G | 9.1% | I32V (ATC→GTC) | lolC → | lipoprotein‑releasing system transmembrane protein |
| RA | 1,249,309 | C→A | 10.4% | G700G (GGG→GGT) | ycgV ← | putative adhesin |
| RA | 1,255,300 | C→A | 11.9% | G320G (GGG→GGT) | dauA ← | C4‑dicarboxylic acid transporter |
| RA | 1,262,289 | G→T | 8.1% | R247L (CGA→CTA) | prmC → | N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2 |
| RA | 1,266,001 | G→T | 8.6% | 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 | 1,268,692 | C→A | 6.9% | intergenic (+34/+10) | chaC → / ← ychN | cation transport regulator/putative sulfur relay protein |
| RA | 1,274,439 | G→T | 9.3% | G343W (GGG→TGG) | narK → | nitrate/nitrite transporter |
| RA | 1,282,249 | A→G | 10.7% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,353,652 | G→A | 7.4% | intergenic (‑208/+95) | puuP ← / ← puuA | putrescine importer/glutamate‑‑putrescine ligase |
| RA | 1,394,938 | T→C | 12.2% | M365V (ATG→GTG) | abgT ← | p‑aminobenzoyl‑glutamate transporter; membrane protein |
| RA | 1,401,323 | G→A | 17.6% | R244W (CGG→TGG) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,417,757 | C→G | 12.3% | pseudogene (300/444 nt) P34R (CCG→CGG) |
rzpR → rzoR → |
pseudogene, Rac prophage; Bacteriophage Rz lysis protein family;Phage or Prophage Related; putative Rac prophage endopeptidase; completely contained in another CDS Rac prophage; putative lipoprotein |
| RA | 1,422,040 | A→G | 14.2% | 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 | 15.8% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 6.9% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,451,079 | C→A | 5.7% | I131I (ATC→ATA) | paaE → | ring 1,2‑phenylacetyl‑CoA epoxidase, NAD(P)H oxidoreductase component |
| RA | 1,461,046 | C→T | 8.7% | pseudogene (1398/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,494,253 | G→T | 8.5% | L152I (CTC→ATC) | ydcK ← | uncharacterized protein |
| RA | 1,510,420 | G→T | 6.5% | V196L (GTG→TTG) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,518,785 | C→A | 6.3% | D485Y (GAT→TAT) | ansP ← | L‑asparagine transporter |
| RA | 1,546,375 | C→T | 8.7% | intergenic (+127/+280) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,546,379 | T→A | 10.7% | intergenic (+131/+276) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,546,381 | G→T | 10.7% | intergenic (+133/+274) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,546,389 | T→G | 9.1% | intergenic (+141/+266) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,546,391 | A→G | 12.1% | intergenic (+143/+264) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,546,395 | T→C | 11.8% | intergenic (+147/+260) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,612,872 | C→A | 6.5% | A98A (GCG→GCT) | marC ← | UPF0056 family inner membrane protein |
| RA | 1,655,096 | A→G | 6.7% | Q95R (CAG→CGG) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,662,087 | T→C | 7.1% | I245M (ATA→ATG) | mlc ← | glucosamine anaerobic growth regulon transcriptional repressor; autorepressor |
| RA | 1,679,322 | G→T | 9.6% | A269A (GCG→GCT) | tus → | inhibitor of replication at Ter, DNA‑binding protein |
| RA | 1,685,784 | A→C | 21.8% | intergenic (+167/+59) | ydgA → / ← uidC | DUF945 family protein/putative outer membrane porin for beta‑glucuronides porin protein |
| RA | 1,691,173 | C→A | 5.5% | G46V (GGG→GTG) | uidR ← | transcriptional repressor |
| RA | 1,692,311 | G→T | 15.7% | intergenic (‑14/+98) | hdhA ← / ← malI | 7‑alpha‑hydroxysteroid dehydrogenase, NAD‑dependent/transcriptional repressor of Mal regulon |
| RA | 1,702,127 | G→T | 8.5% | V318L (GTG→TTG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,725,058 | G→A | 6.1% | G572D (GGT→GAT) | lhr → | putative ATP‑dependent helicase |
| RA | 1,730,002 | G→A | 12.1% | W123* (TGG→TAG) | sodB → | superoxide dismutase, Fe |
| RA | 1,737,280 | C→A | 8.1% | G74C (GGC→TGC) | ribC ← | riboflavin synthase, alpha subunit |
| RA | 1,742,940 | G→T | 9.6% | R518L (CGG→CTG) | ydhS → | putative oxidoreductase |
| RA | 1,759,865 | G→T | 6.6% | L9M (CTG→ATG) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| RA | 1,766,678 | G→T | 8.3% | intergenic (+136/‑91) | ydiM → / → ydiN | MFS superfamily sugar transport 1 family protein/MFS transporter superfamily protein |
| RA | 1,775,444 | C→A | 11.3% | Q263K (CAG→AAG) | ydiR → | putative electron transfer flavoprotein, FAD‑binding subunit |
| RA | 1,780,962 | C→T | 11.8% | P136P (CCG→CCA) | ppsA ← | phosphoenolpyruvate synthase |
| RA | 1,830,122 | G→A | 8.2% | L117L (CTG→CTA) | ynjA → | carboxymuconolactone decarboxylase family protein |
| RA | 1,838,356 | C→A | 7.9% | G258V (GGG→GTG) | ynjI ← | inner membrane protein |
| RA | 1,872,211 | C→A | 7.8% | A80A (GCC→GCA) | yeaP → | diguanylate cyclase |
| RA | 1,893,726 | C→A | 6.6% | P348Q (CCG→CAG) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,894,074 | G→T | 5.7% | G464V (GGG→GTG) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,928,735 | C→A | 10.0% | G43C (GGT→TGT) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,962,099 | G→T | 5.8% | V220V (GTC→GTA) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| RA | 1,978,497 | G→T | 7.3% | P18P (CCC→CCA) | araG ← | fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 2,013,184 | G→T | 7.5% | S29I (AGC→ATC) | fliL → | flagellar biosynthesis protein |
| RA | 2,076,492 | G→T | 13.7% | A86S (GCC→TCC) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,082,354 | C→A | 8.2% | E86* (GAG→TAG) | yeeZ ← | putative epimerase |
| RA | 2,087,506 | G→A | 5.3% | L186L (CTG→CTA) | hisB → | fused histidinol‑phosphatase/imidazoleglycerol‑phosphate dehydratase |
| RA | 2,108,970 | C→A | 7.1% | P136P (CCG→CCT) | wcaM ← | colanic acid biosynthesis protein |
| RA | 2,112,760 | C→A | 10.8% | G294W (GGG→TGG) | wzxC ← | putative colanic acid exporter |
| RA | 2,114,497 | G→A | 8.7% | P180L (CCG→CTG) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,154,362 | G→T | 7.4% | S832S (TCG→TCT) | mdtC → | multidrug efflux system, subunit C |
| RA | 2,271,432 | G→T | 6.0% | C95* (TGC→TGA) | yejG ← | uncharacterized protein |
| RA | 2,315,195 | C→A | 5.9% | T558T (ACC→ACA) | atoS → | sensory histidine kinase in two‑component regulatory system with AtoC |
| RA | 2,334,003 | C→T | 5.5% | G1216S (GGC→AGC) | yfaL ← | adhesin |
| RA | 2,339,166 | C→A | 5.8% | H275N (CAT→AAT) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,368,060 | C→A | 5.5% | L141F (TTG→TTT) | menE ← | O‑succinylbenzoate‑CoA ligase |
| RA | 2,382,131 | C→A | 8.6% | R6R (CGC→CGA) | yfbO → | uncharacterized protein |
| RA | 2,399,955 | C→A | 100% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,408,026 | C→A | 5.6% | R360S (CGC→AGC) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 2,408,061 | C→A | 5.1% | F371L (TTC→TTA) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 2,441,638 | G→T | 7.7% | T94T (ACC→ACA) | prmB ← | N5‑glutamine methyltransferase |
| RA | 2,444,593 | G→A | 9.7% | G157G (GGC→GGT) | yfcR ← | putative fimbrial‑like adhesin protein |
| RA | 2,453,016 | G→T | 7.9% | V311V (GTC→GTA) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| RA | 2,455,842 | C→A | 7.4% | A353E (GCG→GAG) | fadL → | long‑chain fatty acid outer membrane transporter |
| RA | 2,537,490 | G→T | 9.2% | L165M (CTG→ATG) | ucpA ← | furfural resistance protein, putative short‑chain oxidoreductase |
| RA | 2,556,164 | G→T | 9.6% | M94I (ATG→ATT) | yffP → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,607,521 | G→T | 5.9% | G77C (GGC→TGC) | focB → | putative formate transporter |
| RA | 2,624,721 | C→A | 6.4% | G392C (GGC→TGC) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,625,504 | C→T | 7.6% | A131T (GCA→ACA) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,628,149 | C→A | 9.4% | R187S (CGC→AGC) | xseA → | exonuclease VII, large subunit |
| RA | 2,628,801 | G→T | 8.3% | R404L (CGT→CTT) | xseA → | exonuclease VII, large subunit |
| RA | 2,644,979 | C→A | 10.6% | W223L (TGG→TTG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,740,578 | C→A | 17.4% | G193C (GGT→TGT) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,749,911 | C→A | 8.0% | R132S (CGC→AGC) | intA → | CP4‑57 prophage; integrase |
| RA | 2,769,263 | C→G | 6.3% | intergenic (+88/‑15) | ypjI → / → yfjX | pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related/CP4‑57 prophage; putative antirestriction protein |
| RA | 2,769,292 | A→G | 6.4% | T5T (ACA→ACG) | yfjX → | CP4‑57 prophage; putative antirestriction protein |
| RA | 2,769,296 | T→C | 6.3% | Y7H (TAC→CAC) | yfjX → | CP4‑57 prophage; putative antirestriction protein |
| RA | 2,769,306 | T→C | 5.5% | V10A (GTA→GCA) | yfjX → | CP4‑57 prophage; putative antirestriction protein |
| RA | 2,832,793 | G→T | 6.2% | intergenic (‑170/‑90) | ascG ← / → ascF | asc operon transcriptional repressor; prpBC operon repressor/fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
| RA | 2,842,568 | C→A | 6.8% | V11V (GTG→GTT) | hycC ← | hydrogenase 3, membrane subunit |
| RA | 2,860,636 | C→T | 5.1% | R92H (CGC→CAC) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,875,562 | G→T | 8.3% | R145R (CGC→CGA) | casB ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| RA | 2,897,454 | G→T | 10.8% | intergenic (+721/+652) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,906,099 | C→A | 5.6% | P304P (CCG→CCT) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,952,375 | C→T | 7.4% | intergenic (‑132/+44) | ptrA ← / ← recC | protease III/exonuclease V (RecBCD complex), gamma chain |
| RA | 2,960,340 | C→T | 14.3% | G485E (GGG→GAG) | ptsP ← | fused PTS enzyme: PEP‑protein phosphotransferase (enzyme I)/GAF domain containing protein |
| RA | 2,992,134 | G→T | 8.6% | pseudogene (54/1137 nt) | ygeQ ← | pseudogene |
| RA | 2,995,397 | G→T | 6.4% | R565L (CGA→CTA) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 2,999,720 | G→T | 10.2% | E34* (GAA→TAA) | ygeW → | putative carbamoyltransferase |
| RA | 3,034,234 | C→A | 8.0% | D66Y (GAT→TAT) | sdhE ← | flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair |
| RA | 3,074,968 | A→G | 5.2% | N9N (AAT→AAC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,098,414 | C→A | 5.7% | S208* (TCG→TAG) | mltC → | membrane‑bound lytic murein transglycosylase C |
| RA | 3,125,118 | C→A | 6.2% | R217L (CGC→CTC) | yghQ ← | putative inner membrane polysaccharide flippase |
| RA | 3,160,235 | G→A | 5.6% | G281G (GGC→GGT) | ygiS ← | putative inner membrane ABC superfamily transporter permease |
| RA | 3,163,602 | G→A | 6.7% | R139H (CGT→CAT) | qseB → | quorum sensing DNA‑binding response regulator in two‑component regulatory system with QseC |
| RA | 3,164,961 | G→T | 6.3% | V373V (GTG→GTT) | qseC → | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB |
| RA | 3,173,163 | C→A | 6.7% | L21M (CTG→ATG) | ygiB → | DUF1190 family protein |
| RA | 3,192,070 | C→A | 6.2% | G311C (GGT→TGT) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,969 | G→T | 5.9% | S216* (TCG→TAG) | ttdR ← | transcriptional activator of ttdABT |
| RA | 3,217,879 | C→A | 7.9% | L630M (CTG→ATG) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,234,102 | C→A | 5.1% | S267Y (TCT→TAT) | sstT → | sodium:serine/threonine symporter |
| RA | 3,264,900 | C→A | 8.0% | W77L (TGG→TTG) | garK ← | glycerate kinase I |
| RA | 3,312,314 | C→A | 11.1% | R107S (CGC→AGC) | argG → | argininosuccinate synthetase |
| RA | 3,344,014 | G→T | 7.9% | noncoding (79/121 nt) | arcZ → | sRNA positive antisense regulator of rpoS; binds Hfq |
| RA | 3,347,225 | G→T | 7.3% | S62Y (TCC→TAC) | yhcC ← | putative Fe‑S oxidoreductase, Radical SAM superfamily protein |
| RA | 3,357,054 | C→A | 6.1% | R297S (CGC→AGC) | yhcD → | putative outer membrane fimbrial subunit usher protein |
| RA | 3,407,568 | Δ1 bp | 8.3% | coding (346/1158 nt) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,407,569 | Δ1 bp | 8.3% | coding (347/1158 nt) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,407,570 | Δ1 bp | 8.3% | coding (348/1158 nt) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,413,542 | C→A | 9.9% | P17H (CCT→CAT) | yhdX → | putative amino‑acid transporter subunit |
| RA | 3,416,890 | T→G | 11.6% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 15.5% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,428,636 | C→A | 6.2% | S24* (TCA→TAA) | rsmB → | 16S rRNA m(5)C967 methyltransferase, SAM‑dependent |
| RA | 3,434,282 | C→A | 23.9% | G36V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,447,141 | C→A | 7.1% | G49V (GGG→GTG) | gspB ← | part of gsp divergon involved in type II protein secretion |
| RA | 3,484,122 | C→A | 6.8% | G23W (GGG→TGG) | pabA ← | aminodeoxychorismate synthase, subunit II |
| RA | 3,505,502 | C→A | 8.5% | G68C (GGC→TGC) | yhfZ ← | putative DNA‑binding transcriptional regulator |
| RA | 3,554,033 | C→A | 5.4% | V260V (GTG→GTT) | glpG ← | rhomboid intramembrane serine protease |
| RA | 3,632,895 | G→T | 5.4% | L62L (CTC→CTA) | uspB ← | universal stress (ethanol tolerance) protein B |
| RA | 3,660,685 | C→A | 17.4% | D86Y (GAC→TAC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,669,532 | T→C | 8.3% | intergenic (+64/+118) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,533 | C→T | 8.7% | intergenic (+65/+117) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,537 | A→T | 8.2% | intergenic (+69/+113) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,539 | G→C | 8.7% | intergenic (+71/+111) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,540 | A→T | 8.3% | intergenic (+72/+110) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,550 | C→A | 8.3% | intergenic (+82/+100) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,669,573 | Δ1 bp | 6.1% | intergenic (+105/+77) | yhjE → / ← yhjG | MFS superfamily sugar transport 1 family protein/putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,736,472 | C→T | 7.4% | A127V (GCG→GTG) | yiaK → | 2,3‑diketo‑L‑gulonate reductase, NADH‑dependent |
| RA | 3,741,020 | C→A | 5.6% | P193T (CCG→ACG) | lyxK → | L‑xylulose kinase |
| RA | 3,752,197 | G→T | 7.4% | P342Q (CCG→CAG) | selB ← | selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,758,930 | C→A | 10.9% | Q1130K (CAA→AAA) | rhsA → | Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor |
| RA | 3,782,661 | G→T | 5.5% | P261T (CCG→ACG) | waaH ← | LPS(HepIII)‑glucuronic acid glycosyltransferase |
| RA | 3,803,655 | G→A | 5.8% | K157K (AAG→AAA) | coaD → | pantetheine‑phosphate adenylyltransferase |
| RA | 3,825,297 | G→T | 6.7% | G494V (GGT→GTT) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,838,534 | C→A | 5.4% | P404H (CCC→CAC) | ade → | cryptic adenine deaminase |
| RA | 3,857,628 | C→A | 5.4% | R124S (CGC→AGC) | yidP → | UTRA domain‑containing GntR family putative transcriptional regulator |
| RA | 3,890,034 | C→T | 9.1% | intergenic (‑65/‑100) | purP ← / → yieH | adenine permease, high affinity; adenine:H+ symporter/phosphoenolpyruvate and 6‑phosphogluconate phosphatase |
| RA | 3,894,832 | G→A | 10.0% | T250I (ACT→ATT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,909,525 | G→T | 10.3% | P404Q (CCG→CAG) | atpD ← | F1 sector of membrane‑bound ATP synthase, beta subunit |
| RA | 3,930,072 | G→T | 9.5% | A145A (GCG→GCT) | rbsB → | D‑ribose transporter subunit |
| RA | 3,962,595 | C→A | 7.9% | L69M (CTG→ATG) | wzzE → | Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein |
| RA | 3,973,126 | G→T | 6.8% | G389V (GGG→GTG) | wzyE → | putative ECA polysaccharide chain elongation protein |
| RA | 3,995,833 | C→A | 6.6% | T109T (ACG→ACT) | yigF ← | putative inner membrane protein |
| RA | 3,999,848 | G→T | 8.6% | D209Y (GAC→TAC) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,000,028 | G→T | 5.3% | G269W (GGG→TGG) | recQ → | ATP‑dependent DNA helicase |
| RA | 4,005,227 | A→G | 5.4% | T264T (ACA→ACG) L317P (CTG→CCG) |
yigM → metR ← |
putative inner membrane EamA‑like transporter methionine biosynthesis regulon transcriptional regulator |
| RA | 4,012,733 | G→A | 8.5% | K173K (AAG→AAA) | ubiE → | bifunctional 2‑octaprenyl‑6‑methoxy‑1,4‑benzoquinone methylase/ S‑adenosylmethionine:2‑DMK methyltransferase |
| RA | 4,026,677 | G→A | 7.4% | R58H (CGC→CAC) | trkH → | potassium transporter |
| RA | 4,027,494 | G→A | 5.6% | P330P (CCG→CCA) | trkH → | potassium transporter |
| RA | 4,032,027 | G→T | 5.7% | noncoding (1149/2905 nt) | rrlA → | 23S ribosomal RNA of rrnA operon |
| RA | 4,039,627 | C→T | 9.7% | L112L (CTG→CTA) | yihG ← | inner membrane protein, inner membrane acyltransferase |
| RA | 4,042,071 | C→A | 10.4% | S582S (TCC→TCA) | polA → | fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease |
| RA | 4,055,146 | G→A | 9.8% | A208T (GCC→ACC) | yihM → | putative sugar phosphate isomerase |
| RA | 4,059,693 | C→A | 5.8% | G288C (GGC→TGC) | yihP ← | putative transporter |
| RA | 4,059,760 | C→A | 6.0% | Q265H (CAG→CAT) | yihP ← | putative transporter |
| RA | 4,084,018 | A→G | 7.3% | S90P (TCG→CCG) | frvX ← | putative peptidase |
| RA | 4,084,023 | T→A | 6.5% | N88I (AAT→ATT) ‡ | frvX ← | putative peptidase |
| RA | 4,084,024 | T→A | 6.4% | N88Y (AAT→TAT) ‡ | frvX ← | putative peptidase |
| RA | 4,084,025 | C→T | 6.4% | W87* (TGG→TGA) ‡ | frvX ← | putative peptidase |
| RA | 4,084,026 | C→T | 6.4% | W87* (TGG→TAG) ‡ | frvX ← | putative peptidase |
| RA | 4,096,239 | T→C | 5.7% | R164R (CGT→CGC) | cpxP → | inhibitor of the cpx response; periplasmic adaptor protein |
| RA | 4,120,811 | C→T | 5.1% | A350V (GCG→GTG) | metL → | Bifunctional aspartokinase/homoserine dehydrogenase 2 |
| RA | 4,124,260 | G→T | 10.0% | A166A (GCG→GCT) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,126,572 | G→T | 5.8% | P179P (CCG→CCT) | yijE → | EamA‑like transporter family protein |
| RA | 4,135,939 | C→T | 6.1% | L673L (CTG→TTG) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,158,403 | G→T | 8.7% | intergenic (+28/‑166) | gltT → / → rrlB | tRNA‑Glu/23S ribosomal RNA of rrnB operon |
| RA | 4,165,449 | C→T | 12.2% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 12.1% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,172,018 | C→A | 10.3% | V282V (GTC→GTA) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,178,500 | C→T | 74.0% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,217,366 | C→T | 5.8% | A1204V (GCC→GTC) | metH → | homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent |
| RA | 4,225,928 | C→A | 5.3% | S32* (TCG→TAG) | yjbE → | extracellular polysaccharide production threonine‑rich protein |
| RA | 4,248,790 | G→T | 5.7% | W374L (TGG→TTG) | dinF → | oxidative stress resistance protein; putative MATE family efflux pump; UV and mitomycin C inducible protein |
| RA | 4,256,541 | T→G | 8.5% | Y278D (TAT→GAT) ‡ | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,256,543 | T→A | 8.3% | Y278* (TAT→TAA) ‡ | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,256,545 | C→T | 8.0% | P279L (CCG→CTG) | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,256,549:1 | +A | 8.3% | coding (840/1080 nt) | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,256,654 | G→T | 6.9% | Q315H (CAG→CAT) | alr → | alanine racemase, biosynthetic, PLP‑binding |
| RA | 4,315,977 | G→A | 6.2% | intergenic (‑419/+239) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,323,042 | C→A | 6.5% | L16F (TTG→TTT) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| RA | 4,336,274 | G→A | 8.6% | G290G (GGC→GGT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,336,286 | G→A | 8.2% | G286G (GGC→GGT) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,343,566 | C→T | 5.3% | P323P (CCG→CCA) | lysU ← | lysine tRNA synthetase, inducible |
| RA | 4,376,301 | C→A | 14.6% | D963Y (GAC→TAC) | mscM ← | mechanosensitive channel protein, miniconductance |
| RA | 4,422,750 | C→A | 8.6% | G42W (GGG→TGG) | ytfF ← | DMT transporter family inner membrane protein |
| RA | 4,451,855:1 | +T | 9.5% | coding (623/2139 nt) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,457,463 | C→A | 7.0% | R8R (CGG→AGG) | mgtA → | magnesium transporter |
| RA | 4,491,293 | C→A | 6.0% | R73S (CGC→AGC) | yjgZ → | uncharacterized protein |
| RA | 4,503,801 | G→T | 8.1% | R109S (CGC→AGC) | fecB ← | iron‑dicitrate transporter subunit |
| RA | 4,508,684 | C→T | 6.7% | pseudogene (147/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,690 | T→G | 7.6% | pseudogene (153/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,699 | A→G | 7.3% | pseudogene (162/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,702 | T→C | 7.3% | pseudogene (165/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,826 | G→A | 5.3% | pseudogene (289/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,830 | A→G | 5.4% | pseudogene (293/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,551,828 | G→A | 6.1% | A222V (GCG→GTG) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| RA | 4,560,423 | C→A | 6.3% | W323C (TGG→TGT) | yjiR ← | putative DNA‑binding transcriptional regulator/putative aminotransferase |
| RA | 4,589,944 | G→T | 6.7% | T21T (ACC→ACA) | yjjA ← | putative DUF2501 family periplasmic protein |
| RA | 4,593,548 | G→T | 6.3% | W85C (TGG→TGT) | yjjQ → | putative transcriptional regulator |
| RA | 4,597,750 | A→G | 5.2% | N44S (AAC→AGC) | holD → | DNA polymerase III, psi subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2208313 | 2209065 | 753 | 10 [6] | [6] 7 | [mlrA] | [mlrA] |
| * | * | ÷ | CP009273 | 3763089 | 3763224 | 136 | 7 [5] | [6] 8 | [yibV] | [yibV] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 52 (0.950) | 60 (1.090) | 28/250 | NT | 53.6% | 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 | 1203246 = | 23 (0.420) | 21 (0.440) | 15/218 | NT | 57.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 11 (0.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 23 (0.420) | 13 (0.270) | 8/218 | NT | 45.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 11 (0.230) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2283592 | NA (NA) | 8 (0.150) | 4/246 | NT | 12.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2399636 = | 57 (1.060) | coding (485/939 nt) | lrhA | transcriptional repressor of flagellar, motility and chemotaxis genes | |||||