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 | 3,915 | C→T | 14.3% | A61V (GCG→GTG) | thrC → | L‑threonine synthase |
| RA | 45,773 | G→A | 6.4% | intergenic (+23/‑34) | fixX → / → yaaU | putative 4Fe‑4S ferredoxin‑type protein/putative transporter |
| RA | 66,181 | C→T | 11.4% | pseudogene (352/678 nt) | araD ← | pseudogene, truncated |
| RA | 113,252 | C→T | 10.0% | R112H (CGC→CAC) | hofB ← | T2SE secretion family protein; P‑loop ATPase superfamily protein |
| RA | 129,554 | C→A | 8.9% | R485S (CGT→AGT) | acnB → | bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase |
| RA | 168,433 | A→G | 8.9% | Q162R (CAG→CGG) | fhuB → | fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components |
| RA | 179,606 | T→G | 17.4% | F219L (TTT→TTG) | cdaR → | carbohydrate diacid regulon transcriptional regulator; autoregulator |
| RA | 184,946 | G→A | 12.9% | R64R (CGC→CGT) | glnD ← | uridylyltransferase |
| RA | 186,605 | A→G | 18.2% | D82G (GAC→GGC) | rpsB → | 30S ribosomal subunit protein S2 |
| RA | 221,393 | C→T | 5.0% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 5.2% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 5.5% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 5.5% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 9.5% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 9.9% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 11.6% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 10.8% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 11.2% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 264,318 | T→A | 6.2% | V118V (GTA→GTT) ‡ | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 264,320 | C→T | 6.5% | V118I (GTA→ATA) ‡ | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 264,330 | G→C | 7.4% | R114R (CGC→CGG) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 264,333 | A→G | 7.3% | P113P (CCT→CCC) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 264,339 | C→T | 7.2% | Q111Q (CAG→CAA) | ykfA ← | CP4‑6 prophage; putative GTP‑binding protein |
| RA | 275,655 | G→T | 12.6% | pseudogene (14/174 nt) | insI1 → | IS30 transposase;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 352,192 | G→A | 9.7% | R104H (CGC→CAC) | codA → | cytosine/isoguanine deaminase |
| RA | 359,068 | T→C | 12.1% | pseudogene (999/1125 nt) | lacZ ← | pseudogene, truncated |
| RA | 392,152 | G→A | 10.5% | A20T (GCA→ACA) | sbmA → | microcin B17 transporter |
| RA | 467,962 | G→A | 5.6% | intergenic (+89/‑92) | mdlB → / → glnK | putative multidrug transporter subunit of ABC superfamily, ATP‑binding component/nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB |
| RA | 478,387 | A→C | 6.9% | A491A (GCT→GCG) | acrB ← | multidrug efflux system protein |
| RA | 482,717 | C→A | 18.7% | N242K (AAC→AAA) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 488,619 | G→A | 8.0% | A358T (GCA→ACA) | dnaX → | DNA polymerase III/DNA elongation factor III, tau and gamma subunits |
| RA | 505,312 | A→G | 7.4% | A508A (GCT→GCC) | copA ← | copper transporter |
| RA | 520,516 | C→G | 5.5% | Y600* (TAC→TAG) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 521,002 | G→T | 5.3% | E762D (GAG→GAT) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 522,248 | A→T | 5.1% | S1178C (AGC→TGC) | rhsD → | Rhs family putative polymorphic toxin |
| RA | 522,440 | T→A | 8.0% | L1242I (TTA→ATA) ‡ | rhsD → | Rhs family putative polymorphic toxin |
| RA | 522,442 | A→G | 7.8% | L1242L (TTA→TTG) ‡ | rhsD → | Rhs family putative polymorphic toxin |
| RA | 544,949 | C→A | 15.4% | I379I (ATC→ATA) | ylbE → | NO‑induced DUF1116 protein |
| RA | 664,361 | G→T | 19.4% | S44S (TCC→TCA) | rsfS ← | ribosomal silencing factor |
| RA | 693,614 | C→A | 14.7% | M340I (ATG→ATT) | asnB ← | asparagine synthetase B |
| RA | 714,575 | C→A | 6.7% | E448* (GAA→TAA) | speF ← | ornithine decarboxylase isozyme, inducible |
| RA | 727,369 | A→G | 5.6% | A777A (GCA→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,375 | A→G | 5.4% | G779G (GGA→GGG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,989 | C→A | 8.4% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 730,138 | A→G | 16.2% | pseudogene (550/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 730,555 | A→C | 6.3% | pseudogene (967/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 805,444 | G→A | 9.1% | P215P (CCG→CCA) | bioB → | biotin synthase |
| RA | 806,981 | G→A | 7.7% | G382D (GGC→GAC) A2T (GCA→ACA) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| RA | 820,110 | G→A | 8.5% | V9I (GTC→ATC) | ybhQ → | inner membrane protein |
| RA | 820,551 | C→A | 15.4% | L338L (CTG→CTT) | ybhR ← | inner membrane putative ABC superfamily transporter permease |
| RA | 890,257 | G→T | 9.9% | D340Y (GAT→TAT) | potF → | putrescine transporter subunit: periplasmic‑binding component of ABC superfamily |
| RA | 894,638 | A→G | 12.1% | Y222C (TAC→TGC) | rlmC → | 23S rRNA m(5)U747 methyltransferase, SAM‑dependent |
| RA | 944,487 | G→T | 26.7% | P180T (CCC→ACC) | ycaN ← | LysR family putative transcriptional regulator |
| RA | 1,003,849 | C→T | 13.8% | R184* (CGA→TGA) | rlmL → | fused 23S rRNA m(2)G2445 and m(7)G2069 methyltransferase, SAM‑dependent |
| RA | 1,016,418 | C→A | 100% | intergenic (‑43/‑176) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| RA | 1,057,627 | C→A | 8.7% | H125N (CAT→AAT) | torD → | TorA‑maturation chaperone |
| RA | 1,117,532 | G→A | 12.9% | H178Y (CAC→TAC) | pyrC ← | dihydro‑orotase |
| RA | 1,151,105 | G→T | 12.1% | E176* (GAA→TAA) | tmk → | thymidylate kinase |
| RA | 1,159,357 | C→A | 14.9% | V214V (GTC→GTA) | thiK → | thiamine kinase |
| RA | 1,191,676 | C→T | 18.7% | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | 15.1% | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,701 | T→C | 15.6% | L375L (TTA→CTA) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,703 | A→G | 18.6% | L375L (TTA→TTG) ‡ | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,195,727 | G→T | 26.7% | A179E (GCA→GAA) | intE ← | e14 prophage; putative integrase |
| RA | 1,229,969 | G→T | 22.1% | L69M (CTG→ATG) | nhaB ← | sodium:proton antiporter |
| RA | 1,265,441 | T→C | 12.5% | intergenic (+62/+253) | rdlB → / ← ldrC | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB/toxic polypeptide, small |
| RA | 1,265,442 | T→G | 12.5% | intergenic (+63/+252) | rdlB → / ← ldrC | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB/toxic polypeptide, small |
| RA | 1,265,467 | T→G | 12.6% | intergenic (+88/+227) | rdlB → / ← ldrC | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB/toxic polypeptide, small |
| RA | 1,265,505 | A→G | 19.3% | 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 | 1,268,061 | G→A | 11.4% | S33S (TCG→TCA) | chaC → | cation transport regulator |
| RA | 1,282,785:1 | +C | 7.8% | intergenic (‑1/+209) | tyrV ← / ← tyrT | tRNA‑Tyr/tRNA‑Tyr |
| RA | 1,290,647 | G→T | 7.0% | pseudogene (132/183 nt) | insZ ← | pseudogene, transposase homolog |
| RA | 1,335,305 | C→T | 11.8% | A164V (GCC→GTC) | yciM → | envelope integrity maintenance protein; EnvC‑interacting protein |
| RA | 1,396,193 | G→T | 14.5% | T440T (ACC→ACA) | abgB ← | p‑aminobenzoyl‑glutamate hydrolase, B subunit |
| RA | 1,422,150 | C→T | 6.4% | pseudogene (834/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,252 | A→G | 6.3% | 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 | 5.4% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,447,482 | C→T | 9.1% | A140T (GCG→ACG) | paaZ ← | fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,457,369 | G→T | 11.1% | D330Y (GAC→TAC) | paaK → | phenylacetyl‑CoA ligase |
| RA | 1,542,551 | C→T | 11.4% | N298N (AAC→AAT) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,544,826 | T→A | 10.7% | S37T (TCC→ACC) | fdnH → | formate dehydrogenase‑N, Fe‑S (beta) subunit, nitrate‑inducible |
| RA | 1,566,159 | G→A | 12.9% | D48D (GAC→GAT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,587,383 | C→G | 9.6% | pseudogene (4862/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,602,939 | G→A | 10.8% | A114V (GCC→GTC) | yneE ← | bestrophin family putative inner membrane protein |
| RA | 1,648,506 | C→T | 12.1% | R298H (CGC→CAC) | rspA ← | bifunctional D‑altronate/D‑mannonate dehydratase |
| RA | 1,655,529 | T→C | 6.9% | G239G (GGT→GGC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,682,136 | G→T | 10.8% | Q167K (CAG→AAG) | fumA ← | fumarate hydratase (fumarase A), aerobic Class I |
| RA | 1,708,355 | C→T | 11.1% | P444S (CCG→TCG) | dtpA → | dipeptide and tripeptide permease A |
| RA | 1,724,943 | G→A | 13.3% | A534T (GCC→ACC) | lhr → | putative ATP‑dependent helicase |
| RA | 1,755,106 | C→A | 25.2% | G315C (GGT→TGT) | sufD ← | component of SufBCD Fe‑S cluster assembly scaffold |
| RA | 1,770,987 | G→T | 21.1% | D382Y (GAC→TAC) | ydiF → | putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit |
| RA | 1,831,177 | C→T | 8.3% | A283V (GCA→GTA) | ynjB → | putative ABC superfamily transporter periplasmic‑binding protein |
| RA | 1,849,622 | G→A | 12.9% | L203L (CTG→TTG) | ydjG ← | alpha‑Keto reductase, NADH‑dependent; can use methylglyoxal as substrate |
| RA | 1,898,537 | C→T | 7.0% | P129L (CCG→CTG) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,931,287 | C→A | 17.6% | Q127K (CAG→AAG) | yebK → | putative DNA‑binding transcriptional regulator |
| RA | 1,971,475 | A→T | 15.4% | intergenic (‑79/+48) | motA ← / ← flhC | proton conductor component of flagella motor/flagellar class II regulon transcriptional activator, with FlhD |
| RA | 1,971,477 | C→A | 15.4% | intergenic (‑81/+46) | motA ← / ← flhC | proton conductor component of flagella motor/flagellar class II regulon transcriptional activator, with FlhD |
| JC JC | 1,972,762 | IS5 (–) +4 bp | 84.1% | intergenic (‑308/‑469) | flhD ← / → uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| RA | 2,070,418 | C→A | 6.8% | R41S (CGT→AGT) | yeeT → | CP4‑44 prophage; uncharacterized protein |
| RA | 2,074,682 | G→T | 13.3% | P21Q (CCG→CAG) | sbmC ← | DNA gyrase inhibitor |
| RA | 2,103,293 | C→A | 21.1% | Q109H (CAG→CAT) | rfbC ← | dTDP‑4‑deoxyrhamnose‑3,5‑epimerase |
| RA | 2,111,275 | C→A | 5.4% | G204V (GGC→GTC) | wcaK ← | colanic acid biosynthesis protein |
| RA | 2,138,221 | G→T | 11.7% | R492L (CGT→CTT) | yegE → | putative diguanylate cyclase |
| RA | 2,148,537 | C→A | 18.2% | V347V (GTC→GTA) | mdtA → | multidrug efflux system, subunit A |
| RA | 2,163,604 | C→A | 9.8% | pseudogene (45/475 nt) | gatR ← | pseudogene, repressor for gat operon; interrupted by IS3; split galactitol utilization operon repressor, fragment 2; split galactitol utilization operon repressor, interrupted |
| RA | 2,183,987 | C→A | 20.7% | E135* (GAA→TAA) | yehB ← | putative outer membrane protein |
| RA | 2,208,384 | G→T | 19.6% | D14Y (GAT→TAT) | mlrA → | transcriptional activator of csgD and csgBA |
| RA | 2,336,854 | G→A | 10.5% | N265N (AAC→AAT) | yfaL ← | adhesin |
| RA | 2,514,609 | Δ1 bp | 57.1% | intergenic (+2/‑3) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,514,610 | Δ1 bp | 50.0% | intergenic (+3/‑2) | valY → / → lysV | tRNA‑Val/tRNA‑Lys |
| RA | 2,557,321 | T→C | 6.6% | F124S (TTT→TCT) | yffQ → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,588,519 | C→T | 17.4% | A234T (GCA→ACA) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
| RA | 2,650,543 | C→A | 8.8% | A584A (GCG→GCT) | hscA ← | DnaK‑like molecular chaperone specific for IscU |
| RA | 2,650,660 | G→T | 8.5% | G545G (GGC→GGA) | hscA ← | DnaK‑like molecular chaperone specific for IscU |
| RA | 2,682,911 | A→T | 11.1% | 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 | 2,682,916 | C→T | 13.8% | intergenic (‑51/+114) | 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 | 2,818,448 | G→T | 11.1% | T163N (ACC→AAC) | mltB ← | membrane‑bound lytic murein transglycosylase B |
| RA | 2,829,143 | G→T | 8.7% | R548R (CGA→AGA) | hypF ← | carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases |
| RA | 2,841,684 | Δ1 bp | 10.0% | coding (917/1827 nt) | hycC ← | hydrogenase 3, membrane subunit |
| RA | 2,976,578 | C→T | 11.1% | V14I (GTC→ATC) | kduD ← | hexuronate dehydrogenase; hexuronate utilization in high osmolarity |
| RA | 3,052,294 | G→A | 15.4% | L131L (CTG→TTG) | rpiA ← | ribose 5‑phosphate isomerase, constitutive |
| RA | 3,076,158 | G→T | 17.1% | intergenic (+128/+78) | loiP → / ← speB | Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era/agmatinase |
| RA | 3,078,578 | Δ1 bp | 8.5% | coding (693/1977 nt) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,078,582 | Δ1 bp | 8.5% | coding (689/1977 nt) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,078,583 | Δ1 bp | 8.2% | coding (688/1977 nt) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,105,020 | C→A | 7.7% | pseudogene (430/963 nt) | yghE ← | pseudogene, secretion pathway protein, L‑type protein homology; putative general secretion pathway for protein export (GSP) |
| RA | 3,108,071 | C→A | 7.0% | P1467P (CCG→CCT) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,172,163 | G→A | 7.0% | P230P (CCG→CCA) | tolC → | transport channel |
| RA | 3,193,131 | C→T | 13.8% | W398* (TGG→TGA) | ygiF ← | inorganic triphosphatase |
| RA | 3,209,706 | C→A | 6.3% | G49C (GGC→TGC) | yqjH ← | putative siderophore interacting protein |
| RA | 3,210,790 | A→G | 14.3% | intergenic (+29/+125) | yqjI → / ← aer | PadR family putative transcriptional regulator/fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component |
| RA | 3,273,465 | G→A | 7.7% | G398D (GGC→GAC) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,350,922 | G→T | 7.8% | D947Y (GAT→TAT) | gltB → | glutamate synthase, large subunit |
| RA | 3,409,305 | C→A | 7.2% | A305D (GCC→GAC) | acrF → | multidrug efflux system protein |
| RA | 3,432,640 | G→T | 17.4% | R77S (CGT→AGT) | yhdN ← | DUF1992 family protein |
| RA | 3,507,239 | C→A | 11.1% | P170P (CCG→CCT) | gph ← | phosphoglycolate phosphatase |
| RA | 3,604,821 | G→A | 5.9% | C91C (TGC→TGT) | yhhS ← | putative arabinose efflux transporter |
| RA | 3,614,484 | C→A | 5.9% | R645S (CGC→AGC) | rhsB → | Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor |
| RA | 3,621,775 | C→T | 10.0% | R375H (CGT→CAT) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,654,029 | G→T | 14.8% | G86C (GGC→TGC) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,654,031 | Δ1 bp | 14.8% | coding (258/3114 nt) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,654,034 | T→C | 16.0% | N87N (AAT→AAC) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,654,038 | Δ1 bp | 16.0% | coding (265/3114 nt) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,660,812 | A→G | 7.9% | F43F (TTT→TTC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,660,824 | A→G | 8.1% | D39D (GAT→GAC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,699,848 | C→A | 11.4% | Q406H (CAG→CAT) | dppA ← | dipeptide transporter |
| RA | 3,707,804 | G→T | 6.0% | L651M (CTG→ATG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,707,904 | C→A | 10.5% | G617G (GGG→GGT) | bisC ← | biotin sulfoxide reductase |
| RA | 3,750,720 | C→A | 8.9% | A156A (GCG→GCT) | yiaY ← | putative Fe‑containing alcohol dehydrogenase, Pfam00465 family |
| RA | 3,763,387 | G→A | 16.0% | pseudogene (80/87 nt) | yibU → | pseudogene, H repeat‑associated protein |
| RA | 3,772,447 | G→T | 6.0% | V12F (GTT→TTT) | lldR → | dual role activator/repressor for lldPRD operon |
| RA | 3,810,113 | G→T | 9.4% | S26S (TCG→TCT) | yicC → | UPF0701 family protein |
| RA | 3,829,536 | G→T | 10.6% | intergenic (‑247/‑46) | yicJ ← / → selC | putative transporter/tRNA‑Sec |
| RA | 3,888,770 | A→G | 100% | I400I (ATT→ATC) | purP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,918,277 | C→A | 10.5% | Q239H (CAG→CAT) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 4,014,575 | C→A | 13.4% | I330I (ATC→ATA) | ubiB → | regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase |
| RA | 4,074,377 | T→C | 6.9% | H71R (CAT→CGT) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,118,278 | C→A | 9.1% | G16C (GGC→TGC) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,176,229 | G→T | 16.8% | G318C (GGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,410 | A→C | 22.2% | T1045P (ACC→CCC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 28.0% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,226,363 | C→T | 5.5% | G58G (GGC→GGT) | yjbF → | extracellular polysaccharide production lipoprotein |
| RA | 4,264,335 | C→A | 7.3% | Q95K (CAG→AAG) | ssb → | single‑stranded DNA‑binding protein |
| RA | 4,292,529 | G→T | 15.4% | H123N (CAT→AAT) | mdtO ← | membrane translocase (MDR) of MdtNOP efflux pump, PET family |
| RA | 4,302,095 | G→A | 7.0% | C238C (TGC→TGT) | alsR ← | d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR |
| RA | 4,313,407 | C→T | 9.5% | G255S (GGC→AGC) | phnD ← | phosphonate ABC transporter periplasmic binding protein |
| RA | 4,370,695 | C→T | 11.5% | A481T (GCA→ACA) | frdA ← | fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit |
| RA | 4,452,322 | G→A | 19.0% | G52G (GGC→GGT) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,498,909 | G→T | 5.4% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,528,788 | C→A | 7.4% | Q177H (CAG→CAT) | nanC ← | N‑acetylnuraminic acid outer membrane channel protein |
| RA | 4,574,059 | C→A | 9.9% | pseudogene (2574/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| RA | 4,627,688 | C→A | 12.5% | S392R (AGC→AGA) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB, regulator of the CreBC regulon |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 80555 | 80673 | 119 | 3 [0] | [1] 3 | leuL/leuO | leu operon leader peptide/global transcription factor |
| * | * | ÷ | CP009273 | 454338 | 455409 | 1072 | 4 [2] | [1] 3 | [lon] | [lon] |
| * | * | ÷ | CP009273 | 455497 | 456677 | 1181 | 3 [2] | [1] 7 | lon | DNA‑binding ATP‑dependent protease La |
| * | * | ÷ | CP009273 | 578896 | 579170 | 275 | 5 [2] | [2] 3 | [appY] | [appY] |
| * | * | ÷ | CP009273 | 1192598 | 1192653 | 56 | 3 [2] | [1] 3 | ymfD | e14 prophage; putative SAM‑dependent methyltransferase |
| * | * | ÷ | CP009273 | 1459372 | 1459483 | 112 | 3 [2] | [2] 3 | [ynbG] | [ynbG] |
| * | * | ÷ | CP009273 | 1524275 | 1524375 | 101 | 3 [2] | [2] 4 | ydcD | uncharacterized protein |
| * | * | ÷ | CP009273 | 2027119 | 2027155 | 37 | 3 [2] | [2] 3 | [rseX] | [rseX] |
| * | * | ÷ | CP009273 | 2027277 | 2027418 | 142 | 3 [2] | [1] 3 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein |
| * | * | ÷ | CP009273 | 2099589 | 2099699 | 111 | 3 [2] | [2] 3 | wbbH | O‑antigen polymerase |
| * | * | ÷ | CP009273 | 2897053 | 2897174 | 122 | 3 [2] | [2] 3 | ygcE/queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| * | * | ÷ | CP009273 | 2988548 | 2988683 | 136 | 3 [2] | [0] 4 | [ygeN] | [ygeN] |
| * | * | ÷ | CP009273 | 3448820 | 3448865 | 46 | 4 [2] | [0] 9 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | CP009273 | 3763054 | 3763192 | 139 | 5 [2] | [0] 3 | [yibV] | [yibV] |
| * | * | ÷ | CP009273 | 3797620 | 3797774 | 155 | 4 [2] | [1] 3 | waaS | lipopolysaccharide core biosynthesis protein |
| * | * | ÷ | CP009273 | 4037430 | 4037469 | 40 | 3 [1] | [0] 4 | dsbA/yihF | periplasmic protein disulfide isomerase I/DUF945 family protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 13 (0.420) | 26 (0.840) | 13/250 | NT | 66.7% | 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 = | 4 (0.130) | 6 (0.220) | 4/218 | NT | 53.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 7 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 4 (0.130) | 11 (0.410) | 8/218 | NT | 67.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 7 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2399639 | 22 (0.710) | 6 (0.190) | 5/250 | NT | 21.4% | 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 | |||||