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 | 287 | Δ1 bp | 6.4% | intergenic (+32/‑50) | thrL → / → thrA | thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 291 | A→T | 6.3% | intergenic (+36/‑46) | thrL → / → thrA | thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 293:1 | +G | 6.4% | intergenic (+38/‑44) | thrL → / → thrA | thr operon leader peptide/Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 6,305 | A→G | 6.6% | I52T (ATC→ACC) | yaaA ← | peroxide resistance protein, lowers intracellular iron |
| RA | 71,999 | T→G | 10.2% | L217V (TTG→GTG) | yabI → | DedA family inner membrane protein |
| RA | 83,587 | A→C | 6.5% | intergenic (‑58/+35) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 83,590 | G→T | 5.6% | intergenic (‑61/+32) | leuA ← / ← leuL | 2‑isopropylmalate synthase/leu operon leader peptide |
| RA | 151,688 | C→G | 9.0% | V182L (GTA→CTA) | yadL ← | putative fimbrial‑like adhesin protein |
| RA | 164,581 | A→C | 22.6% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 173,453 | T→A | 5.5% | intergenic (+9/+149) | fhuB → / ← hemL | iron(3+)‑hydroxamate import ABC transporter permease/glutamate‑1‑semialdehyde aminotransferase (aminomutase) |
| RA | 238,523 | G→T | 5.9% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 238,532 | C→A | 6.8% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| RA | 238,535 | G→T | 10.0% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,247 | A→T | 5.6% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 624,610 | A→T | 12.1% | intergenic (‑100/‑275) | fepB ← / → entC | ferrienterobactin ABC transporter periplasmic binding protein/isochorismate synthase 1 |
| RA | 644,030 | A→G | 5.1% | intergenic (‑63/+167) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 644,034 | T→C | 5.3% | intergenic (‑67/+163) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 644,036 | A→T | 5.1% | intergenic (‑69/+161) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 644,038 | G→A | 5.4% | intergenic (‑71/+159) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 644,042 | C→T | 5.4% | intergenic (‑75/+155) | rnk ← / ← rna | regulator of nucleoside diphosphate kinase/ribonuclease I |
| RA | 659,204 | C→T | 5.1% | intergenic (+54/+47) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,205 | A→T | 5.2% | intergenic (+55/+46) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,206 | A→T | 5.5% | intergenic (+56/+45) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 659,207 | A→G | 5.3% | intergenic (+57/+44) | tatE → / ← lipA | TatABCE protein translocation system subunit/lipoate synthase |
| RA | 781,238 | T→A | 5.5% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
| RA | 843,216 | G→T | 14.6% | M295I (ATG→ATT) | rlmF → | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| RA | 847,213 | A→T | 5.4% | intergenic (‑94/+45) | glnP ← / ← glnH | glutamine transporter subunit/glutamine transporter subunit |
| RA | 847,214 | T→A | 5.5% | intergenic (‑95/+44) | glnP ← / ← glnH | glutamine transporter subunit/glutamine transporter subunit |
| RA | 847,215 | A→T | 5.1% | intergenic (‑96/+43) | glnP ← / ← glnH | glutamine transporter subunit/glutamine transporter subunit |
| RA | 857,576 | T→C | 5.5% | intergenic (+21/+220) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,578 | C→G | 5.4% | intergenic (+23/+218) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 857,580 | G→A | 5.8% | intergenic (+25/+216) | ybiT → / ← ybiU | ABC‑F family putative regulatory ATPase/DUF1479 family protein |
| RA | 993,254 | A→G | 5.3% | intergenic (+20/+23) | pepN → / ← ssuB | aminopeptidase N/aliphatic sulfonate ABC transporter ATPase |
| RA | 993,255 | A→C | 5.5% | intergenic (+21/+22) | pepN → / ← ssuB | aminopeptidase N/aliphatic sulfonate ABC transporter ATPase |
| RA | 993,258 | G→T | 5.2% | intergenic (+24/+19) | pepN → / ← ssuB | aminopeptidase N/aliphatic sulfonate ABC transporter ATPase |
| RA | 993,259 | C→T | 5.5% | intergenic (+25/+18) | pepN → / ← ssuB | aminopeptidase N/aliphatic sulfonate ABC transporter ATPase |
| RA | 1,286,965 | A→G | 6.2% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,324,837 | A→C | 6.1% | Y31S (TAT→TCT) ‡ | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,324,838 | T→A | 5.7% | Y31* (TAT→TAA) ‡ | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,324,839 | G→T | 6.2% | E32* (GAA→TAA) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,351,228 | G→C | 11.3% | intergenic (‑189/+179) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,552,078 | G→A | 6.5% | intergenic (+87/+320) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,079 | C→A | 6.1% | intergenic (+88/+319) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,085 | G→T | 7.0% | intergenic (+94/+313) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,086 | A→C | 6.9% | intergenic (+95/+312) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,092 | T→G | 5.7% | intergenic (+101/+306) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,093 | T→C | 5.8% | intergenic (+102/+305) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,256 | G→A | 5.5% | intergenic (+265/+142) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,257 | C→A | 5.6% | intergenic (+266/+141) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,263 | G→T | 6.3% | intergenic (+272/+135) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,264 | A→C | 6.2% | intergenic (+273/+134) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,270 | T→G | 5.6% | intergenic (+279/+128) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,552,271 | T→C | 5.6% | intergenic (+280/+127) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,708,709 | T→A | 7.9% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→A | 8.6% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→T | 8.0% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,810,062 | T→C | 5.3% | intergenic (+14/‑149) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,065 | T→G | 5.2% | intergenic (+17/‑146) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,066 | C→A | 6.1% | intergenic (+18/‑145) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,810,069 | G→A | 5.3% | intergenic (+21/‑142) | yniC → / → ydjM | 2‑deoxyglucose‑6‑P phosphatase/inner membrane protein regulated by LexA |
| RA | 1,864,758 | G→A | 9.2% | intergenic (+24/+24) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,763 | A→T | 9.4% | intergenic (+29/+19) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,864,768 | T→C | 10.4% | intergenic (+34/+14) | yeaD → / ← yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| RA | 1,865,682 | G→C | 5.4% | intergenic (‑46/+44) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,177,228 | C→A | 8.8% | intergenic (‑24/+284) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,229 | G→T | 5.3% | intergenic (‑25/+283) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,234 | C→A | 17.4% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 14.9% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,187,314 | C→G | 5.8% | intergenic (+16/+66) | rcnB → / ← yehA | periplasmic modulator of Ni and Co efflux/putative fimbrial‑like adhesin protein |
| RA | 2,229,177 | A→C | 13.7% | intergenic (+112/+261) | yohP → / ← dusC | uncharacterized protein/tRNA‑dihydrouridine synthase C |
| RA | 2,304,522 | G→T | 5.4% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,523 | G→C | 7.0% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,649 | C→T | 5.9% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,856 | A→C | 5.1% | intergenic (+463/+252) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,311,616 | C→T | 5.6% | intergenic (‑82/+30) | apbE ← / ← ompC | putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C |
| RA | 2,311,619 | A→G | 5.3% | intergenic (‑85/+27) | apbE ← / ← ompC | putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,383,956 | A→T | 6.6% | intergenic (+32/+39) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,383,959 | A→T | 6.3% | intergenic (+35/+36) | elaD → / ← yfbK | protease, capable of cleaving an AMC‑ubiquitin model substrate/Von Willebrand factor domain putative lipoprotein |
| RA | 2,432,985 | A→G | 5.5% | intergenic (‑43/+27) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,990 | G→C | 5.9% | intergenic (‑48/+22) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,995 | C→T | 5.5% | intergenic (‑53/+17) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,470,427 | C→A | 10.2% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,470,436 | C→A | 8.5% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
| RA | 2,653,367 | G→A | 6.4% | intergenic (+28/‑488) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,372 | T→C | 6.2% | intergenic (+33/‑483) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,692 | A→T | 5.4% | intergenic (+353/‑163) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,693 | A→G | 5.4% | intergenic (+354/‑162) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,695 | A→T | 6.1% | intergenic (+356/‑160) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,697 | C→T | 5.3% | intergenic (+358/‑158) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,653,698 | A→T | 5.9% | intergenic (+359/‑157) | sseA → / → ryfA | 3‑mercaptopyruvate sulfurtransferase/novel sRNA, function unknown |
| RA | 2,691,169 | A→T | 5.5% | noncoding (172/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,171 | T→A | 5.7% | noncoding (170/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,173 | A→T | 6.1% | noncoding (168/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,716,030 | T→G | 5.6% | intergenic (+20/+36) | eamB → / ← grcA | cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor |
| RA | 2,716,033 | C→A | 5.5% | intergenic (+23/+33) | eamB → / ← grcA | cysteine and O‑acetylserine exporter/autonomous glycyl radical cofactor |
| RA | 2,724,095 | C→A | 5.1% | intergenic (+13/‑33) | pssA → / → yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| RA | 2,724,097 | T→A | 5.3% | intergenic (+15/‑31) | pssA → / → yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| RA | 2,724,099 | T→G | 5.3% | intergenic (+17/‑29) | pssA → / → yfiM | phosphatidylserine synthase; CDP‑diacylglycerol‑serine O‑phosphatidyltransferase/putative lipoprotein |
| RA | 2,725,844 | G→T | 6.4% | intergenic (‑98/+225) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,778,124 | A→C | 5.5% | intergenic (+342/+22) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter |
| RA | 2,817,916 | T→G | 6.2% | intergenic (‑56/+143) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,046 | A→G | 5.3% | intergenic (‑186/+13) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,907,998 | A→T | 5.3% | intergenic (‑57/+31) | eno ← / ← pyrG | enolase/CTP synthetase |
| RA | 3,004,963 | T→A | 7.1% | E275V (GAG→GTG) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 3,046,050 | T→G | 7.9% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase/glycine decarboxylase, PLP‑dependent, subunit P of glycine cleavage complex |
| RA | 3,087,396 | T→G | 6.6% | F231V (TTC→GTC) | metK → | S‑adenosylmethionine synthetase |
| RA | 3,180,506 | A→C | 5.1% | E29A (GAG→GCG) | ygiC → | ATP‑Grasp family ATPase |
| RA | 3,234,506 | G→A | 5.7% | intergenic (‑51/+233) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,234,507 | A→T | 5.6% | intergenic (‑52/+232) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,234,508 | T→C | 5.6% | intergenic (‑53/+231) | higB ← / ← rlmG | mRNA interferase toxin of the HigB‑HigA toxin‑antitoxin system/23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,239,609 | T→G | 11.2% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,610 | C→G | 5.0% | intergenic (+65/‑334) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,630 | A→T | 11.9% | intergenic (+85/‑314) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,270,082 | A→C | 5.3% | intergenic (+480/+134) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,288,033 | T→G | 5.4% | intergenic (+23/‑57) | yraH → / → yraI | putative fimbrial‑like adhesin protein/putative periplasmic pilin chaperone |
| RA | 3,324,952 | A→G | 5.4% | intergenic (‑41/+49) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,955 | A→G | 5.4% | intergenic (‑44/+46) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,956 | C→T | 5.5% | intergenic (‑45/+45) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,324,959 | C→T | 5.5% | intergenic (‑48/+42) | folP ← / ← ftsH | 7,8‑dihydropteroate synthase/protease, ATP‑dependent zinc‑metallo |
| RA | 3,423,390 | C→T | 6.2% | intergenic (+196/+33) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,396 | T→G | 6.4% | intergenic (+202/+27) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,397 | T→G | 5.9% | intergenic (+203/+26) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,398 | C→A | 6.1% | intergenic (+204/+25) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,399 | C→A | 6.0% | intergenic (+205/+24) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,423,405 | A→G | 6.1% | intergenic (+211/+18) | yhdZ → / ← rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| RA | 3,439,588 | G→C | 8.5% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 8.4% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,608,695 | C→G | 10.5% | intergenic (+46/+56) | zntA → / ← tusA | zinc, cobalt and lead efflux system/mnm(5)‑s(2)U34‑tRNA 2‑thiolation sulfurtransferase |
| RA | 3,657,599 | T→A | 6.8% | intergenic (+32/+387) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,601 | G→C | 6.8% | intergenic (+34/+385) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,657,603 | T→A | 6.8% | intergenic (+36/+383) | hdeD → / ← arrS | acid‑resistance membrane protein/antisense sRNA ArrS, function unknown |
| RA | 3,728,109 | A→C | 7.8% | D421E (GAT→GAG) | xylB ← | xylulokinase |
| RA | 3,728,125 | T→G | 5.2% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
| RA | 3,781,051 | C→G | 5.4% | intergenic (+34/‑164) | lldD → / → trmL | L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent |
| JC | 3,815,859 | Δ82 bp | 33.1% | [rph]–[rph] | [rph], [rph] | |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,908,506 | C→G | 5.8% | intergenic (‑140/+43) | pstB ← / ← pstA | phosphate ABC transporter ATPase/phosphate ABC transporter permease |
| RA | 3,959,501 | T→A | 8.4% | intergenic (+56/+31) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 3,959,515 | T→A | 9.8% | intergenic (+70/+17) | ilvC → / ← ppiC | ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,004,029 | C→A | 8.0% | M50I (ATG→ATT) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,015,093 | G→T | 10.7% | D681Y (GAT→TAT) | metE → | 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase |
| RA | 4,051,259 | G→T | 5.8% | noncoding (224/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,051,262 | A→C | 5.0% | noncoding (227/245 nt) | csrC → | CsrC sRNA sequesters CsrA, a carbon flux regulator |
| RA | 4,060,264 | A→C | 5.2% | intergenic (+34/‑183) | typA → / → yihL | GTP‑binding protein/putative DNA‑binding transcriptional regulator |
| RA | 4,183,669 | G→T | 11.2% | G809C (GGT→TGT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,184,809 | G→T | 8.9% | G1189C (GGT→TGT) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,207,576 | A→G | 5.6% | intergenic (‑44/‑571) | purH ← / → rrsE | IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon |
| RA | 4,296,060 | C→T | 29.2% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,155 | T→C | 7.2% | intergenic (+361/+281) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,307,294 | A→T | 5.8% | L169Q (CTG→CAG) | alsK ← | D‑allose kinase |
| RA | 4,307,298 | G→A | 5.8% | P168S (CCC→TCC) | alsK ← | D‑allose kinase |
| RA | 4,366,854 | T→G | 5.5% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,366,855 | C→A | 5.3% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,479,012 | A→T | 5.3% | intergenic (+123/+22) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,016 | G→C | 5.2% | intergenic (+127/+18) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,479,020 | A→T | 5.3% | intergenic (+131/+14) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,520,500 | Δ1 bp | 5.8% | intergenic (‑176/+171) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| RA | 4,520,504:1 | +T | 5.7% | intergenic (‑180/+167) | yjhU ← / ← yjhF | putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 100% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 772974 | 774240 | 1267 | 239 [234] | [236] 244 | [cydA]–[cydX] | [cydA],cydB,[cydX] |
| * | * | ÷ | NC_000913 | 1037673 | 1039370 | 1698 | 239 [234] | [238] 241 | cbdA–[cbdB] | cbdA,[cbdB] |
| * | * | ÷ | NC_000913 | 2403898 | 2404669 | 772 | 240 [235] | [237] 245 | nuoB–[nuoA] | nuoB,[nuoA] |
| * | * | ÷ | NC_000913 | 3423722–3424590 | 3424590 | 1–869 | 242 [235] | [235] 245 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 15580 | NA (NA) | 14 (0.040) | 8/270 | NT | NA | noncoding (194/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 15601 | NA (NA) | noncoding (215/1345 nt) | IS186 | repeat region | |||||
| * | ? | NC_000913 | = 224598 | NA (NA) | 3 (0.010) | 3/256 | NT | NA | noncoding (828/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 224641 | NA (NA) | noncoding (871/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 274384 = | NA (NA) | 4 (0.010) | 4/266 | NT | NA | noncoding (766/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274422 = | NA (NA) | noncoding (728/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 8 (0.020) | 5/254 | NT | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 381689 | NA (NA) | 3 (0.010) | 3/254 | NT | NA | noncoding (430/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381743 | NA (NA) | noncoding (484/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 382323 | NA (NA) | 4 (0.010) | 4/262 | NT | NA | noncoding (1064/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382348 | NA (NA) | noncoding (1089/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 445266 | NA (NA) | 6 (0.020) | 5/262 | NT | NA | noncoding (67/87 nt) | REP40 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP40 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913 | = 445281 | NA (NA) | noncoding (82/87 nt) | REP40 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP40 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||
| * | ? | NC_000913 | = 699504 | NA (NA) | 10 (0.030) | 6/258 | NT | NA | noncoding (80/98 nt) | RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2684124 = | NA (NA) | noncoding (8/98 nt) | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 715264 = | NA (NA) | 10 (0.030) | 5/258 | NT | NA | noncoding (1/98 nt) | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP65 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2549491 = | NA (NA) | noncoding (26/98 nt) | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 815603 = | NA (NA) | 13 (0.040) | 7/258 | NT | NA | noncoding (19/97 nt) | RIP73 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP73 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 3639299 | NA (NA) | noncoding (91/98 nt) | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1028361 = | NA (NA) | 11 (0.030) | 8/244 | NT | NA | intergenic (+2/+43) | yccU/hspQ | putative CoA‑binding protein/heat shock protein involved in degradation of mutant DnaA; hemimethylated oriC DNA‑binding protein |
| ? | NC_000913 | 1028395 = | NA (NA) | intergenic (+36/+9) | yccU/hspQ | putative CoA‑binding protein/heat shock protein involved in degradation of mutant DnaA; hemimethylated oriC DNA‑binding protein | |||||
| * | ? | NC_000913 | 1068372 = | NA (NA) | 4 (0.010) | 3/258 | NT | NA | noncoding (19/98 nt) | RIP92 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP92 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2684124 = | NA (NA) | noncoding (8/98 nt) | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1097426 = | NA (NA) | 21 (0.050) | 14/268 | NT | 16.9% | intergenic (+597/+139) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913 | 1097455 = | 105 (0.270) | intergenic (+626/+110) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1113435 = | NA (NA) | 11 (0.030) | 7/258 | NT | NA | noncoding (19/98 nt) | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2684124 = | NA (NA) | noncoding (8/98 nt) | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 1207790 = | 244 (0.630) | 97 (0.280) | 59/240 | NT | 28.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 263 (0.760) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 234 (0.600) | 118 (0.340) | 81/240 | NT | 33.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 263 (0.760) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 333 (0.880) | 156/264 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1327735 = | NA (NA) | 10 (0.030) | 10/256 | NT | NA | intergenic (+8/+32) | rluB/btuR | 23S rRNA pseudouridine(2605) synthase/cob(I)yrinic acid a,c‑diamide adenosyltransferase |
| ? | NC_000913 | 1327758 = | NA (NA) | intergenic (+31/+9) | rluB/btuR | 23S rRNA pseudouridine(2605) synthase/cob(I)yrinic acid a,c‑diamide adenosyltransferase | |||||
| * | ? | NC_000913 | = 2304536 | 382 (0.980) | 17 (0.040) | 11/266 | NT | 5.8% | noncoding (120/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences |
| ? | NC_000913 | = 2304673 | 181 (0.470) | noncoding (257/655 nt) | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | REP161 (repetitive extragenic palindromic) element; contains 12 REP sequences | |||||
| * | ? | NC_000913 | = 2538614 | NA (NA) | 6 (0.020) | 4/258 | NT | NA | noncoding (80/98 nt) | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP174 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | = 3639299 | NA (NA) | noncoding (91/98 nt) | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 2684117 = | NA (NA) | 11 (0.030) | 7/258 | NT | NA | noncoding (1/98 nt) | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913 | 2684142 = | NA (NA) | noncoding (26/98 nt) | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP186 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | = 2817942 | 338 (0.870) | 26 (0.080) | 15/232 | NT | 8.0% | intergenic (‑82/+117) | argQ/argZ | tRNA‑Arg/tRNA‑Arg |
| ? | NC_000913 | 2818492 = | 308 (0.930) | noncoding (58/77 nt) | argV | tRNA‑Arg | |||||
| * | ? | NC_000913 | = 3392102 | 458 (1.170) | 19 (0.060) | 19/206 | NT | 5.3% | noncoding (27/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences |
| ? | NC_000913 | 3392377 = | 335 (1.140) | noncoding (302/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | |||||
| * | ? | NC_000913 | 4542682 = | 307 (0.790) | 18 (0.050) | 16/254 | NT | 5.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 322 (0.880) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 310 (0.790) | 26 (0.070) | 17/254 | NT | 7.8% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 322 (0.880) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||