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 | 19,860 | A→T | 15.6% | L152Q (CTG→CAG) | insB1 ← | IS1 transposase B |
| RA | 46,650 | G→T | 9.1% | A282S (GCA→TCA) | yaaU → | putative transporter |
| RA | 60,953 | C→T | 7.3% | R771H (CGT→CAT) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 114,781:1 | +A | 8.6% | coding (352/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,781:2 | +A | 8.6% | coding (352/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,781:3 | +T | 8.6% | coding (352/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,782 | G→A | 8.6% | G117G (GGC→GGT) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,784:1 | +A | 8.6% | coding (349/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,784:2 | +A | 8.6% | coding (349/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,784:3 | +A | 8.6% | coding (349/894 nt) | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,785 | C→A | 8.6% | T116T (ACG→ACT) ‡ | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,786 | G→C | 8.4% | T116R (ACG→AGG) ‡ | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,791 | C→T | 8.6% | L114L (CTG→CTA) ‡ | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 114,792 | A→T | 8.7% | L114Q (CTG→CAG) ‡ | nadC ← | quinolinate phosphoribosyltransferase |
| RA | 153,184 | C→A | 7.4% | E63* (GAA→TAA) | yadN ← | putative fimbrial‑like adhesin protein |
| RA | 221,373:1 | +G | 9.0% | noncoding (1116/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,380 | T→A | 9.1% | noncoding (1123/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,390 | Δ1 bp | 9.3% | noncoding (1133/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,391 | G→A | 9.3% | noncoding (1134/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,393 | C→T | 9.6% | noncoding (1136/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,395 | G→A | 9.4% | noncoding (1138/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,397 | C→T | 9.5% | noncoding (1140/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,398 | C→T | 9.5% | noncoding (1141/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,402 | A→C | 9.9% | noncoding (1145/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,407 | A→T | 10.4% | noncoding (1150/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,412 | A→T | 10.5% | noncoding (1155/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,420 | A→G | 10.9% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 16.9% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 17.2% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 23.7% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 21.7% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 20.0% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 22.9% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 245,377 | C→A | 8.8% | pseudogene (1181/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| RA | 274,938 | T→A | 5.2% | Q152L (CAG→CTG) | insB1 ← | IS1 transposase B |
| RA | 295,695 | T→G | 5.7% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 335,782 | A→G | 5.1% | intergenic (+328/‑94) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 370,602 | G→A | 6.9% | intergenic (+265/‑313) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,617 | Δ1 bp | 5.6% | intergenic (+280/‑298) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,618 | Δ1 bp | 5.6% | intergenic (+281/‑297) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,619 | T→G | 5.6% | intergenic (+282/‑296) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,621 | Δ1 bp | 6.2% | intergenic (+284/‑294) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,626 | Δ1 bp | 6.2% | intergenic (+289/‑289) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,627 | Δ1 bp | 7.0% | intergenic (+290/‑288) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,628 | Δ1 bp | 6.7% | intergenic (+291/‑287) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,632 | A→G | 7.6% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,658 | T→C | 7.9% | intergenic (+321/‑257) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,659 | T→A | 7.7% | intergenic (+322/‑256) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 385,480 | T→A | 7.5% | intergenic (‑297/‑227) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 393,386 | G→A | 10.2% | G20E (GGG→GAG) | yaiW → | putative lipoprotein |
| RA | 436,987 | C→A | 19.9% | intergenic (‑188/‑18) | xseB ← / → thiI | exonuclease VII small subunit/tRNA s(4)U8 sulfurtransferase |
| RA | 459,279 | G→T | 7.7% | intergenic (+37/‑114) | ppiD → / → ybaV | periplasmic folding chaperone, has an inactive PPIase domain/putative competence‑suppressing periplasmic helix‑hairpin‑helix DNA‑binding protein |
| RA | 573,883 | G→C | 11.0% | T107T (ACG→ACC) R34P (CGG→CCG) |
rzpD → rzoD → |
DLP12 prophage; putative murein endopeptidase DLP12 prophage; putative lipoprotein |
| RA | 727,369 | A→G | 6.1% | A777A (GCA→GCG) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 727,375 | A→G | 6.2% | 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 | 7.5% | pseudogene (550/1521 nt) | rhsO → | pseudogene, Rhs family protein |
| RA | 731,587 | G→T | 7.6% | R161L (CGA→CTA) | ybfC → | putative periplasmic protein |
| RA | 733,211 | T→A | 6.0% | pseudogene (931/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 733,372 | T→C | 7.8% | pseudogene (1092/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 733,384 | C→G | 15.7% | pseudogene (1104/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 734,165 | C→T | 5.9% | F206F (TTC→TTT) | ybfD → | H repeat‑associated putative transposase |
| RA | 811,110 | C→T | 7.5% | intergenic (+107/+85) | uvrB → / ← ybhK | excinulease of nucleotide excision repair, DNA damage recognition component/putative NAD(P)‑binding transferase |
| RA | 833,739 | G→T | 6.3% | R58R (CGC→CGA) | ybiI ← | DksA‑type zinc finger protein |
| RA | 839,517 | Δ1 bp | 6.5% | coding (1420/2226 nt) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 839,518 | Δ1 bp | 6.5% | coding (1419/2226 nt) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 839,519 | Δ1 bp | 6.5% | coding (1418/2226 nt) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 839,520 | Δ1 bp | 6.0% | coding (1417/2226 nt) | ybiO ← | mechanosensitive channel protein, intermediate conductance |
| RA | 849,308 | G→A | 6.8% | R69H (CGC→CAC) | ybiR → | putative transporter |
| RA | 857,390 | C→A | 5.3% | A225S (GCC→TCC) | ybiW ← | putative pyruvate formate lyase |
| RA | 882,776 | C→A | 7.2% | R7L (CGT→CTT) | ybjJ ← | putative transporter |
| RA | 900,616 | G→T | 7.3% | G83V (GGT→GTT) | amiD → | 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent; OM lipoprotein |
| RA | 904,382 | G→A | 5.8% | D123D (GAC→GAT) | ltaE ← | L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 940,636:1 | +G | 5.8% | coding (378/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 940,636:2 | +G | 5.8% | coding (378/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 940,636:3 | +C | 5.8% | coding (378/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 940,638:1 | +T | 6.2% | coding (376/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 940,638:2 | +A | 6.2% | coding (376/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 940,638:3 | +G | 6.2% | coding (376/627 nt) | ycaC ← | putative isochorismatase family hydrolase |
| RA | 965,548 | G→T | 6.2% | R235L (CGT→CTT) | ycaQ → | DUF1006 family protein with C‑terminal wHTH domain |
| RA | 980,627 | C→A | 6.1% | C180F (TGC→TTC) | aspC ← | aspartate aminotransferase, PLP‑dependent |
| RA | 1,074,375 | C→A | 6.1% | intergenic (‑37/‑386) | putA ← / → putP | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase/proline:sodium symporter |
| RA | 1,134,840 | T→C | 5.4% | L336P (CTG→CCG) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,161,605 | C→A | 12.5% | T22K (ACA→AAA) | ndh → | respiratory NADH dehydrogenase 2/cupric reductase |
| RA | 1,169,398 | G→A | 5.3% | T8M (ACG→ATG) | mfd ← | transcription‑repair coupling factor |
| RA | 1,178,411 | G→T | 6.9% | V222V (GTC→GTA) | potC ← | polyamine transporter subunit |
| RA | 1,282,249 | A→G | 9.2% | 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 | 6.9% | intergenic (+515/+25) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,323,001 | G→T | 7.0% | V123V (GTC→GTA) | yciK ← | putative EmrKY‑TolC system oxoacyl‑(acyl carrier protein) reductase |
| RA | 1,354,830 | G→T | 6.7% | A112A (GCC→GCA) | puuA ← | glutamate‑‑putrescine ligase |
| RA | 1,422,040 | A→G | 12.1% | 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 | 12.8% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,150 | C→T | 7.6% | 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 | 5.9% | pseudogene (732/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,426,270 | A→G | 5.4% | K989E (AAA→GAA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,437,441 | C→T | 7.7% | A45V (GCA→GTA) | ydbH → | putative membrane‑anchored protein, function unknown |
| RA | 1,445,629 | G→T | 7.3% | intergenic (‑23/+225) | tynA ← / ← paaZ | tyramine oxidase, copper‑requiring/fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,447,443 | G→A | 10.2% | H153Y (CAT→TAT) | paaZ ← | fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase |
| RA | 1,460,819 | G→A | 10.5% | pseudogene (1171/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,484,659 | C→A | 11.4% | pseudogene (312/750 nt) | gapC ← | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment) |
| RA | 1,491,267 | C→T | 8.0% | S52L (TCA→TTA) | opgD → | osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein |
| RA | 1,507,299 | C→T | 5.9% | R76W (CGG→TGG) | ydcT → | putative spermidine/putrescine transporter subunit |
| RA | 1,515,524 | G→A | 5.5% | A600V (GCG→GTG) | yncD ← | putative iron outer membrane transporter |
| RA | 1,527,173 | C→T | 7.9% | Y367Y (TAC→TAT) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,527,189 | A→G | 7.7% | T373A (ACG→GCG) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,564,253 | A→G | 6.7% | L165P (CTG→CCG) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,574,849 | C→T | 15.4% | G67S (GGC→AGC) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,582,609 | C→A | 7.1% | G163V (GGA→GTA) | ydeS ← | putative fimbrial‑like adhesin protein |
| RA | 1,630,830 | A→G | 10.2% | intergenic (‑206/‑183) | nohQ ← / → ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| RA | 1,754,887 | T→A | 10.5% | M388L (ATG→TTG) | sufD ← | component of SufBCD Fe‑S cluster assembly scaffold |
| RA | 1,770,867 | T→C | 5.0% | S342P (TCA→CCA) | ydiF → | putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit |
| RA | 1,869,685 | G→A | 10.2% | A50V (GCA→GTA) | yeaM ← | putative DNA‑binding transcriptional regulator |
| RA | 1,875,761 | G→T | 6.6% | S102R (AGC→AGA) | dmlR ← | transcriptional activator of dmlA |
| RA | 1,906,184 | A→G | 5.1% | F217S (TTC→TCC) | htpX ← | putative endopeptidase |
| RA | 1,913,736 | Δ1 bp | 5.8% | coding (1970/2634 nt) | yebT → | MCE domain protein |
| RA | 1,913,737 | Δ1 bp | 5.8% | coding (1971/2634 nt) | yebT → | MCE domain protein |
| RA | 1,913,738 | Δ1 bp | 5.8% | coding (1972/2634 nt) | yebT → | MCE domain protein |
| RA | 1,913,739 | Δ1 bp | 5.8% | coding (1973/2634 nt) | yebT → | MCE domain protein |
| RA | 1,913,740 | Δ1 bp | 5.8% | coding (1974/2634 nt) | yebT → | MCE domain protein |
| RA | 1,941,588 | A→G | 7.5% | Y16H (TAC→CAC) | ruvC ← | component of RuvABC resolvasome, endonuclease |
| RA | 1,941,589 | G→A | 8.0% | G15G (GGC→GGT) | ruvC ← | component of RuvABC resolvasome, endonuclease |
| RA | 1,944,310 | A→G | 5.5% | F157S (TTC→TCC) | aspS ← | aspartyl‑tRNA synthetase |
| RA | 1,952,263 | G→T | 10.0% | H43N (CAC→AAC) | torY ← | TMAO reductase III (TorYZ), cytochrome c‑type subunit |
| RA | 2,001,467 | C→A | 15.7% | A35A (GCG→GCT) | yedD ← | lipoprotein |
| RA | 2,004,485 | G→T | 8.8% | P135P (CCG→CCT) | yedL → | putative acyl transferase |
| RA | 2,064,944 | T→C | 6.7% | noncoding (149/204 nt) | isrC → | novel sRNA, CP4‑44; putative prophage remnant |
| RA | 2,064,946:1 | +A | 6.3% | noncoding (151/204 nt) | isrC → | novel sRNA, CP4‑44; putative prophage remnant |
| RA | 2,064,946:2 | +C | 6.3% | noncoding (151/204 nt) | isrC → | novel sRNA, CP4‑44; putative prophage remnant |
| RA | 2,064,946:3 | +A | 6.3% | noncoding (151/204 nt) | isrC → | novel sRNA, CP4‑44; putative prophage remnant |
| RA | 2,064,949 | C→T | 6.2% | noncoding (154/204 nt) | isrC → | novel sRNA, CP4‑44; putative prophage remnant |
| RA | 2,093,894 | C→A | 7.4% | A286S (GCA→TCA) | gnd ← | 6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,126,266 | G→T | 11.8% | L205M (CTG→ATG) | wcaA ← | putative glycosyl transferase |
| RA | 2,167,353 | C→T | 10.2% | L135L (TTG→TTA) | gatC ← | galactitol PTS permease ‑ GatC subunit |
| RA | 2,201,723:1 | +G | 5.4% | coding (278/1137 nt) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,201,723:2 | +C | 5.4% | coding (278/1137 nt) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,201,723:3 | +T | 5.4% | coding (278/1137 nt) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,201,723:4 | +G | 5.4% | coding (278/1137 nt) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,201,723:5 | +C | 5.4% | coding (278/1137 nt) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,213,979 | T→C | 7.3% | Q497R (CAG→CGG) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,276,396 | T→C | 6.0% | intergenic (+116/+23) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,402 | Δ1 bp | 5.9% | intergenic (+122/+17) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,403 | Δ1 bp | 5.9% | intergenic (+123/+16) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,404 | Δ1 bp | 6.1% | intergenic (+124/+15) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,406 | Δ1 bp | 6.3% | intergenic (+126/+13) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,407 | Δ1 bp | 6.5% | intergenic (+127/+12) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,408 | Δ1 bp | 6.6% | intergenic (+128/+11) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,409 | Δ1 bp | 6.6% | intergenic (+129/+10) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,276,410 | Δ1 bp | 6.6% | intergenic (+130/+9) | rplY → / ← yejK | 50S ribosomal subunit protein L25/spermidine nucleoid‑associated protein |
| RA | 2,391,037 | G→T | 5.7% | P870T (CCG→ACG) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,393,971 | G→C | 5.2% | T355R (ACG→AGG) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,393,974 | Δ1 bp | 5.2% | coding (1061/1338 nt) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,393,975 | Δ1 bp | 5.2% | coding (1060/1338 nt) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,393,976 | Δ1 bp | 5.2% | coding (1059/1338 nt) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,399,955 | C→A | 100% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,439,357 | C→T | 9.8% | Q169Q (CAG→CAA) | mepA ← | murein DD‑endopeptidase |
| RA | 2,457,796 | T→C | 6.2% | K231E (AAA→GAA) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,483,212 | G→T | 9.6% | P152T (CCT→ACT) | yfdV ← | putative transporter |
| RA | 2,593,307 | G→T | 9.7% | G15C (GGT→TGT) | gcvR → | transcriptional repressor, regulatory protein accessory to GcvA |
| RA | 2,615,169 | G→T | 9.8% | G205V (GGT→GTT) | purM → | phosphoribosylaminoimidazole synthetase |
| RA | 2,661,478 | C→T | 7.1% | G260R (GGA→AGA) | hcaR ← | hca operon transcriptional regulator |
| RA | 2,663,580 | G→T | 5.3% | G397V (GGG→GTG) | hcaE → | 3‑phenylpropionate dioxygenase, large (alpha) subunit |
| RA | 2,699,643 | C→A | 11.7% | A281S (GCA→TCA) | lepA ← | back‑translocating elongation factor EF4, GTPase |
| RA | 2,707,703 | C→T | 7.7% | intergenic (+114/+95) | srmB → / ← yfiE | ATP‑dependent RNA helicase/putative DNA‑binding transcriptional regulator |
| RA | 2,719,426 | T→C | 16.6% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,461 | C→A | 5.7% | E358* (GAA→TAA) | clpB ← | protein disaggregation chaperone |
| RA | 2,771,529 | T→C | 9.6% | V1519V (GTA→GTG) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,816,372 | C→A | 17.3% | A253S (GCT→TCT) | recA ← | DNA recombination and repair protein; ssDNA‑dependent ATPase; synaptase; ssDNA and dsDNA binding protein forming filaments; ATP‑dependent homologous DNA strand exchanger; recombinase A; LexA autocleavage cofactor |
| RA | 2,821,435 | G→T | 5.5% | V114L (GTG→TTG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,823,738 | G→T | 7.8% | G189G (GGG→GGT) | srlQ → | D‑arabinose 5‑phosphate isomerase |
| RA | 2,824,259 | G→T | 10.0% | Q464K (CAG→AAG) | norR ← | anaerobic nitric oxide reductase DNA‑binding transcriptional activator |
| RA | 2,825,440 | A→G | 6.1% | L70P (CTG→CCG) | norR ← | anaerobic nitric oxide reductase DNA‑binding transcriptional activator |
| RA | 2,873,415 | C→T | 5.3% | R111H (CGC→CAC) | casE ← | CRISPR RNA precursor cleavage enzyme; CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| RA | 3,005,901 | T→A | 7.6% | intergenic (+149/+72) | yqeA → / ← yqeB | putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,037,084:1 | +G | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,084:2 | +G | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,084:3 | +C | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,084:4 | +G | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,084:5 | +C | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,084:6 | +G | 5.3% | coding (64/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,086 | G→C | 5.3% | Q22H (CAG→CAC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,088:1 | +C | 5.3% | coding (68/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,088:2 | +A | 5.3% | coding (68/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,088:3 | +G | 5.3% | coding (68/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,088:4 | +G | 5.3% | coding (68/1440 nt) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,037,234 | C→A | 6.1% | H72N (CAC→AAC) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,064,718 | T→G | 13.6% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,106,358 | C→A | 8.8% | intergenic (‑58/+68) | yghF ← / ← yghG | pseudogene, secretion pathway protein, C‑type protein homology;putative transport; Not classified; putative general secretion pathway for protein export (GSP)/secretin (GspDbeta) OM localization lipoprotein pilotin |
| RA | 3,135,976 | C→T | 5.8% | A125T (GCT→ACT) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,142,666 | G→A | 5.8% | L55L (CTC→CTT) | yqhA ← | UPF0114 family putative inner membrane protein |
| RA | 3,158,532 | C→T | 6.4% | L267L (CTG→CTA) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,169,995 | C→T | 8.9% | A66A (GCG→GCA) | cpdA ← | 3',5' cAMP phosphodiesterase |
| RA | 3,237,555 | C→A | 6.5% | P182P (CCG→CCT) | uxaC ← | uronate isomerase |
| RA | 3,263,315 | T→C | 12.6% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,284,921 | G→T | 7.8% | A74A (GCG→GCT) | yraK → | putative fimbrial‑like adhesin protein |
| RA | 3,308,353 | C→T | 5.1% | A341T (GCA→ACA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,327,782 | G→A | 7.4% | L238L (CTG→CTA) | ispB → | octaprenyl diphosphate synthase |
| RA | 3,403,099 | C→A | 11.8% | A224D (GCC→GAC) | prmA → | methyltransferase for 50S ribosomal subunit protein L11 |
| RA | 3,416,890 | T→G | 10.8% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 13.5% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,446,133 | G→A | 7.3% | T51T (ACC→ACT) | rplC ← | 50S ribosomal subunit protein L3 |
| RA | 3,464,590 | G→A | 7.6% | T33T (ACC→ACT) | tufA ← | translation elongation factor EF‑Tu 1 |
| RA | 3,469,331 | C→A | 10.0% | V157F (GTC→TTC) | yheO ← | putative PAS domain‑containing DNA‑binding transcriptional regulator |
| RA | 3,589,089 | C→A | 5.2% | Q225H (CAG→CAT) | livH ← | leucine/isoleucine/valine transporter subunit |
| RA | 3,594,840 | C→G | 6.4% | E203Q (GAA→CAA) | ftsX ← | inner membrane putative ABC superfamily transporter permease |
| 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 | 13.4% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,686,001 | C→T | 5.3% | D866N (GAT→AAT) | bcsA ← | cellulose synthase, catalytic subunit |
| RA | 3,702,353 | A→G | 5.3% | W495R (TGG→CGG) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,782,486 | C→A | 5.3% | W319L (TGG→TTG) | waaH ← | LPS(HepIII)‑glucuronic acid glycosyltransferase |
| RA | 3,804,818 | C→A | 5.2% | A73S (GCC→TCC) | rpmB ← | 50S ribosomal subunit protein L28 |
| RA | 3,813,247 | C→A | 6.6% | L428L (CTG→CTT) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,912,503 | G→A | 5.2% | P239S (CCG→TCG) | atpA ← | F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 3,917,110 | G→T | 5.3% | S628R (AGC→AGA) | mnmG ← | 5‑methylaminomethyl‑2‑thiouridine modification at tRNA U34 |
| RA | 3,936,724 | T→A | 9.0% | intergenic (+15/‑71) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 3,936,730 | C→T | 6.2% | intergenic (+21/‑65) | rrsC → / → gltU | 16S ribosomal RNA of rrnC operon/tRNA‑Glu |
| RA | 3,971,455 | T→C | 5.9% | S191P (TCC→CCC) | wecF → | TDP‑Fuc4NAc:lipidIIFuc4NAc transferase |
| RA | 4,030,856 | A→T | 14.9% | intergenic (+161/‑23) | alaT → / → rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon |
| RA | 4,143,523 | A→C | 8.1% | intergenic (‑497/+101) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,165,449 | C→T | 34.6% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 34.5% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,177,142 | A→G | 24.0% | D622G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,500 | C→T | 27.0% | R1075C (CGT→TGT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,199,631 | T→A | 7.5% | intergenic (+15/‑71) | rrsE → / → gltV | 16S ribosomal RNA of rrnE operon/tRNA‑Glu |
| RA | 4,202,979 | A→C | 17.1% | noncoding (12/120 nt) | rrfE → | 5S ribosomal RNA of rrnE operon |
| RA | 4,239,325:1 | +A | 13.0% | intergenic (+86/‑157) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,328 | C→A | 12.4% | intergenic (+89/‑154) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,329 | G→C | 16.8% | intergenic (+90/‑153) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,332 | T→A | 11.8% | intergenic (+93/‑150) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,333 | G→C | 12.0% | intergenic (+94/‑149) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,335 | Δ1 bp | 12.2% | intergenic (+96/‑147) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,337 | A→C | 12.0% | intergenic (+98/‑145) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,338 | A→C | 14.8% | intergenic (+99/‑144) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,339 | T→C | 11.1% | intergenic (+100/‑143) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,345 | C→T | 11.3% | intergenic (+106/‑137) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,239,359 | T→C | 9.8% | intergenic (+120/‑123) | lamB → / → malM | maltose outer membrane porin (maltoporin)/maltose regulon periplasmic protein |
| RA | 4,315,765 | A→G | 7.6% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,316,036:1 | +G | 6.0% | intergenic (‑478/+180) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,343,151 | C→T | 8.7% | V462M (GTG→ATG) | lysU ← | lysine tRNA synthetase, inducible |
| RA | 4,369,772 | C→A | 5.9% | G188V (GGT→GTT) | frdB ← | fumarate reductase (anaerobic), Fe‑S subunit |
| RA | 4,370,978 | C→T | 6.1% | L386L (CTG→CTA) | frdA ← | fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit |
| RA | 4,399,395 | G→A | 7.0% | G102S (GGC→AGC) | rlmB → | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 4,405,345 | G→T | 10.8% | M418I (ATG→ATT) | aidB → | DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,423,658 | C→T | 10.4% | A62T (GCA→ACA) | qorB ← | NAD(P)H:quinone oxidoreductase |
| RA | 4,442,581 | C→T | 13.6% | P65L (CCC→CTC) | ytfT → | inner membrane putative ABC superfamily sugar transporter permease |
| RA | 4,449,187 | T→C | 6.9% | intergenic (+59/‑120) | pmbA → / → cybC | putative antibiotic peptide MccB17 maturation peptidase/pseudogene, truncated cytochrome b562; cytochrome b(562) |
| RA | 4,498,909 | G→T | 5.1% | pseudogene (84/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,826 | G→A | 5.1% | pseudogene (289/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,830 | A→G | 5.3% | pseudogene (293/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,577,448 | G→T | 7.4% | G228V (GGC→GTC) | mrr → | methylated adenine and cytosine restriction protein |
| RA | 4,578,122 | G→T | 6.9% | H187Q (CAC→CAA) | yjiA ← | GTP‑binding protein, putative GTPase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2208347 | 2209079 | 733 | 9 [7] | [6] 8 | [mlrA] | [mlrA] |
| * | * | ÷ | CP009273 | 2463643 | 2463814 | 172 | 11 [7] | [6] 8 | gtrS | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| * | * | ÷ | CP009273 | 3448799 | 3448865 | 67 | 9 [5] | [7] 20 | 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 | 335746 = | 134 (2.010) | 11 (0.170) | 6/246 | NT | 7.6% | noncoding (279/358 nt) | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP23 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | CP009273 | 372778 = | NA (NA) | intergenic (+11/+213) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 360104 = | 51 (0.760) | 62 (0.930) | 27/248 | NT | 54.9% | 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 | 54 (1.120) | 15 (0.340) | 5/162 | NT | 23.6% | 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 | = 370414 | 81 (1.210) | 6 (0.130) | 3/174 | NT | 9.9% | noncoding (29/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | = 372848 | 52 (1.110) | noncoding (58/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | = 370486 | 85 (1.760) | 10 (0.230) | 7/164 | NT | 11.4% | noncoding (101/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | 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 | 1203246 = | 18 (0.270) | 34 (0.590) | 19/216 | NT | 70.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 13 (0.220) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 19 (0.280) | 25 (0.430) | 11/216 | NT | 62.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 13 (0.220) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||