mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 38,950 | G→A | P56S (CCG→TCG) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 109,960 | G→A | R561H (CGT→CAT) | secA → | protein translocation ATPase |
| RA | 128,115 | G→A | A68A (GCG→GCA) | lpd → | lipoamide dehydrogenase |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 283,362 | G→T | W54C (TGG→TGT) | yagF → | D‑xylonate dehydratase |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 305,486 | G→A | F444F (TTC→TTT) | ecpD ← | fimbrial adhesin EcpD |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 314,109 | G→A | intergenic (‑867/‑1182) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 315,439 | G→A | R50H (CGC→CAC) | insE1 → | IS3 element protein InsE |
| RA | 317,019 | G→A | intergenic (+566/+707) | insF1 → / ← rclC | IS3 element protein InsF/DUF417 domain‑containing inner membrane protein RclC |
| RA | 320,976 | G→A | E250E (GAG→GAA) | rclR → | DNA‑binding transcriptional activator RclR |
| RA | 334,699 | G→A | F108F (TTC→TTT) | yahC ← | uncharacterized protein YahC |
| RA | 335,395 | G→A | G39E (GGG→GAG) | yahD → | ankyrin repeat‑containing protein YahD |
| RA | 338,327 | G→A | M1M (ATG→ATA) † | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 338,415 | G→A | V31M (GTG→ATG) | yahG → | DUF1116 domain‑containing protein YahG |
| RA | 339,935 | C→T | A56V (GCC→GTC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,941 | C→T | T58I (ACT→ATT) | yahH → | putative uncharacterized protein YahH |
| RA | 339,958 | G→A | D64N (GAC→AAC) | yahH → | putative uncharacterized protein YahH |
| RA | 340,333 | G→A | V57I (GTC→ATC) | yahI → | carbamate kinase‑like protein YahI |
| RA | 351,695 | G→A | E161K (GAA→AAA) | prpD → | 2‑methylcitrate dehydratase |
| RA | 352,701 | G→A | intergenic (+35/‑5) | prpD → / → prpE | 2‑methylcitrate dehydratase/propionyl‑CoA synthetase |
| RA | 353,604 | G→A | G300E (GGG→GAG) | prpE → | propionyl‑CoA synthetase |
| RA | 355,256 | G→A | G112D (GGT→GAT) | codB → | cytosine transporter |
| RA | 356,109 | G→A | L396L (CTG→CTA) | codB → | cytosine transporter |
| RA | 361,896 | G→A | intergenic (‑36/+30) | lacA ← / ← lacY | galactoside O‑acetyltransferase/lactose permease |
| RA | 363,407 | G→A | Q967* (CAA→TAA) | lacZ ← | beta‑galactosidase |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 488,122 | G→A | A529A (GCG→GCA) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 488,151 | G→A | G539D (GGT→GAT) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 488,699 | G→A | A722T (GCA→ACA) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 509,517 | C→T | E621E (GAG→GAA) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 544,861 | C→G | L144L (CTG→CTC) | allC ← | allantoate amidohydrolase |
| RA | 587,661 | G→A | S107S (TCC→TCT) | ybcH ← | putative exopolysaccharide secretion system auxiliary component |
| JC JC | 607,765 | IS150 (+) +3 bp | noncoding (26‑28/60 nt) | sokE ← | small RNA SokE |
| MC JC | 679,777 | Δ8,074 bp | IS5‑mediated | [ybeU]–gltI | [ybeU], djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| JC JC | 729,860 | IS150 (–) +3 bp | coding (278‑280/4194 nt) | rhsC → | rhs element protein RhsC |
| RA | 806,081 | G→A | L401L (CTG→TTG) | ybhC ← | outer membrane lipoprotein YbhC |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 855,674 | G→A | A24V (GCG→GTG) | ldtB ← | L,D‑transpeptidase LdtB |
| RA | 863,304 | G→A | L70L (CTG→TTG) | ybiY ← | putative pyruvate formate‑lyase activating enzyme YbiY |
| RA | 869,418 | G→A | R3K (AGA→AAA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 871,045 | G→A | V27I (GTC→ATC) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 873,115 | G→A | R46H (CGC→CAC) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 884,344 | G→A | G224G (GGG→GGA) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 897,642 | G→A | V187I (GTC→ATC) | potI → | putrescine ABC transporter membrane subunit PotI |
| RA | 909,012 | G→A | L95L (CTG→TTG) | ltaE ← | low‑specificity L‑threonine aldolase |
| JC JC | 927,393 | IS2 (–) +5 bp | coding (36‑40/705 nt) | aat ← | leucyl/phenylalanyl‑tRNA‑‑protein transferase |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| JC JC | 972,851 | IS2 (–) +5 bp | coding (547‑551/780 nt) | elyC ← | envelope biogenesis factor |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,070,014 | A→G | L114P (CTG→CCG) | rutF ← | FMN reductase RutF |
| RA | 1,078,342 | G→T | R181S (CGC→AGC) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,150,616 | C→T | L297L (CTG→TTG) | fabD → | [acyl‑carrier‑protein] S‑malonyltransferase |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| JC JC | 1,186,598 | IS150 (–) +3 bp | coding (755‑757/1227 nt) | pepT → | peptidase T |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| JC JC | 1,234,887 | IS2 (+) +5 bp | intergenic (‑170/‑47) | nhaB ← / → fadR | Na(+):H(+) antiporter NhaB/DNA‑binding transcriptional dual regulator FadR |
| RA | 1,253,002 | C→T | intergenic (+17/+83) | dhaR → / ← ycgV | DNA‑binding transcriptional dual regulator DhaR/putative autotransporter adhesin YcgV |
| RA | 1,276,230 | C→T | P463P (CCG→CCA) | narX ← | sensor histidine kinase NarX |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,234 | T→G | L18R (CTA→CGA) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,315,384 | G→A | Y129Y (TAC→TAT) | yciF ← | DUF892 domain‑containing protein YciF |
| RA | 1,317,129 | G→C | Q32E (CAG→GAG) | trpA ← | tryptophan synthase subunit alpha |
| RA | 1,322,325 | G→A | L208F (CTC→TTC) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,356,932 | G→A | T60I (ACC→ATC) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,366,433 | G→A | G295D (GGC→GAC) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| MC JC | 1,381,790 | Δ14,254 bp | IS5‑mediated | ompG–ynaI | ompG, ycjW, ycjX, ycjF, tyrR, tpx, ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI |
| RA | 1,400,978 | C→T | G266S (GGT→AGT) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| JC JC | 1,461,938 | IS150 (–) +4 bp | coding (1046‑1049/1206 nt) | paaJ → | beta‑ketoadipyl‑CoA thiolase |
| JC JC | 1,492,142 | IS150 (–) +3 bp | noncoding (24‑26/57 nt) | sokB → | putative small regulatory RNA antitoxin SokB |
| RA | 1,501,192 | C→T | P207L (CCT→CTT) | tehA → | tellurite resistance protein |
| RA | 1,510,161 | G→A | Q53Q (CAG→CAA) | ydcR → | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YdcR |
| RA | 1,514,172 | C→T | R114R (CGC→CGT) | ydcU → | putative ABC transporter membrane subunit YdcU |
| RA | 1,517,461 | C→T | L25F (CTT→TTT) | ortT → | orphan toxin OrtT |
| RA | 1,531,755 | A→G | intergenic (‑1251/‑61) | yncO ← / → ydcC | protein YncO/H repeat‑associated putative transposase YdcC |
| JC JC | 1,579,695 | IS5 (+) +4 bp | coding (1093‑1096/1158 nt) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,603,321 | C→T | L101L (CTC→CTT) | lsrC → | Autoinducer‑2 ABC transporter membrane subunit LsrC |
| RA | 1,604,223 | C→T | G59G (GGC→GGT) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,604,840 | C→T | S265F (TCC→TTC) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,605,533 | C→T | S161S (AGC→AGT) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,606,464 | C→T | A122V (GCC→GTC) | lsrF → | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| RA | 1,608,089 | C→T | A248A (GCC→GCT) | tam → | trans‑aconitate 2‑methyltransferase |
| RA | 1,610,381 | A→G | S100S (AGT→AGC) | uxaB ← | tagaturonate reductase |
| RA | 1,632,034 | C→T | Q84Q (CAG→CAA) | ydfJ ← | putative transporter YdfJ |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| JC JC | 1,656,194 | IS2 (–) +5 bp | coding (11‑15/561 nt) | speG → | spermidine N‑acetyltransferase |
| RA | 1,695,900 | C→T | A58T (GCA→ACA) | uidA ← | beta‑glucuronidase |
| RA | 1,701,372 | C→T | A139V (GCT→GTT) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,734,167 | G→A | intergenic (‑66/‑268) | grxD ← / → mepH | glutaredoxin 4/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase MepH |
| JC JC | 1,743,375 | IS1 (+) +8 bp | intergenic (‑133/‑75) | ribC ← / → mdtK | riboflavin synthase/multidrug efflux pump MdtK |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,783,681 | G→A | E235E (GAG→GAA) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,907,451 | IS2 (+) +5 bp | coding (137‑141/144 nt) | yobF ← | DUF2527 domain‑containing protein YobF |
| RA | 1,963,862 | C→T | E397K (GAG→AAG) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | 1,963,973 | C→T | E360K (GAA→AAA) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | 1,964,853 | C→T | Q66Q (CAG→CAA) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | 1,974,896 | C→T | V143V (GTG→GTA) V143V (GTG→GTA) |
cheA ← cheA ← |
chemotaxis protein CheA chemotaxis protein CheA |
| RA | 1,975,279 | C→T | A16T (GCG→ACG) | cheA ← | chemotaxis protein CheA |
| RA | 1,977,100 | C→T | V14I (GTT→ATT) | motA ← | motility protein A |
| RA | 1,987,499 | C→A | intergenic (+71/+8) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 1,987,988 | G→A | intergenic (‑29/‑234) | azuC ← / → yecR | uncharacterized protein AzuC/lipoprotein YecR |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| JC | 2,041,058 | (TATAAG)1→2 | coding (576/636 nt) | msrQ → | membrane‑bound flavocytochrome MsrQ |
| RA | 2,072,723 | C→T | V395V (GTC→GTT) | flu → | self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,074,441 | G→A | S968N (AGC→AAC) | flu → | self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,076,399 | G→A | R31H (CGT→CAT) | yeeS → | RadC‑like JAB domain‑containing protein YeeS |
| RA | 2,076,909 | G→A | W31* (TGG→TGA) | yeeT → | DUF987 domain‑containing protein YeeT |
| RA | 2,077,731 | G→A | A55T (GCA→ACA) | cbtA → | cytoskeleton‑binding toxin CbtA |
| RA | 2,103,351 | G→A | pseudogene (39/446 nt) | wbbL ← | interrupted rhamnosyltransferase WbbL |
| RA | 2,188,087 | T→C | T110A (ACG→GCG) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,188,711 | A→G | Y734H (TAT→CAT) | yehB ← | putative fimbrial usher protein YehB |
| RA | 2,195,035 | G→A | A246T (GCG→ACG) | metG → | methionine‑‑tRNA ligase |
| RA | 2,216,871 | G→A | R179R (CGC→CGT) | yehX ← | glycine betaine ABC transporter ATP binding subunit YehX |
| RA | 2,219,653 | G→A | intergenic (‑172/+39) | osmF ← / ← bglX | glycine betaine ABC transporter periplasmic binding protein OsmF/beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,248,076 | C→T | G153S (GGT→AGT) | lysP ← | lysine:H(+) symporter |
| RA | 2,264,483 | G→A | T207T (ACG→ACA) | setB → | sugar exporter SetB |
| RA | 2,264,637 | G→A | G259R (GGG→AGG) | setB → | sugar exporter SetB |
| RA | 2,284,395 | G→C | R7P (CGC→CCC) | lapC → | lipopolysaccharide signal transducer LapC |
| RA | 2,294,130 | G→A | L259L (CTG→TTG) | ccmF ← | holocytochrome c synthase CcmF component |
| RA | 2,311,176 | G→A | A120V (GCG→GTG) | ftp ← | FAD:protein FMN transferase |
| RA | 2,316,917 | G→A | intergenic (+90/+110) | rcsB → / ← rcsC | DNA‑binding transcriptional activator RcsB/histidine kinase RcsC |
| JC JC | 2,319,848 | IS2 (+) +5 bp | coding (25‑29/2850 nt) | rcsC ← | histidine kinase RcsC |
| JC JC | 2,320,126 | IS2 (–) +5 bp | coding (84‑88/1827 nt) | atoS → | sensor histidine kinase AtoS |
| RA | 2,320,839 | T→C | L266P (CTG→CCG) | atoS → | sensor histidine kinase AtoS |
| RA | 2,358,366 | G→A | N160N (AAC→AAT) | yfaU ← | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| RA | 2,361,166 | T→A | T83T (ACA→ACT) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,382,718 | G→A | M2I (ATG→ATA) | elaD → | protease ElaD |
| RA | 2,384,808 | C→T | K305K (AAG→AAA) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,386,800 | G→A | G314D (GGT→GAT) | yfbL → | putative peptidase YfbL |
| RA | 2,410,419 | G→A | L312L (CTG→TTG) | yfbS ← | putative transporter YfbS |
| RA | 2,417,231 | G→A | D51N (GAT→AAT) | yfcC → | putative transporter YfcC |
| RA | 2,428,433 | G→A | A65V (GCG→GTG) | ubiX ← | flavin prenyltransferase |
| RA | 2,432,054 | G→A | P297S (CCA→TCA) | folC ← | bifunctional folylpolyglutamate synthetase/dihydrofolate synthetase |
| RA | 2,446,640 | G→T | G278G (GGC→GGA) | aroC ← | chorismate synthase |
| RA | 2,454,633 | G→A | intergenic (‑2297/+450) | yfcS ← / ← yfcV | putative fimbrial chaperone YfcS/putative fimbrial protein YfcV |
| RA | 2,463,652 | G→A | R214H (CGT→CAT) | yfdF → | protein YfdF |
| RA | 2,466,572 | G→A | A10T (GCA→ACA) | intS → | prophage CPS‑53 integrase |
| RA | 2,482,646 | G→A | P232S (CCC→TCC) | emrK ← | tripartite efflux pump membrane fusion protein EmrK |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| RA | 2,506,876 | G→A | T340I (ACC→ATC) | fryC ← | putative PTS enzyme IIC component FryC |
| RA | 2,551,581 | G→A | A49V (GCG→GTG) | yfeZ ← | putative inner membrane protein |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,707,579 | G→T | L75I (CTT→ATT) | rseC ← | protein RseC |
| JC JC | 2,771,871 | IS2 (–) +5 bp | coding (280‑284/315 nt) | yfjU ← | putative arsenate reductase‑like protein YfjU |
| RA | 2,803,048 | G→T | A567A (GCG→GCT) | nrdE → | ribonucleoside‑diphosphate reductase 2 subunit alpha |
| RA | 2,894,892 | C→T | intergenic (+121/+27) | ygcP → / ← ygcQ | putative anti‑terminator regulatory protein/putative flavoprotein |
| RA | 2,895,577 | C→T | G68D (GGC→GAC) | ygcQ ← | putative flavoprotein |
| RA | 2,895,651 | C→T | Q43Q (CAG→CAA) | ygcQ ← | putative flavoprotein |
| RA | 2,896,161 | C→T | G132E (GGG→GAG) | ygcR ← | putative flavoprotein |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| MC JC | 3,102,311 | Δ27,835 bp | IS5‑mediated | [trmB]–[yghO] | 24 genes [trmB], mutY, yggX, mltC, nupG, speC, yqgH, yqgA, pheV, yghD, yghE, yqhJ, yghF, yghG, pppA, yghJ, glcA, glcB, glcG, glcF, glcE, glcD, glcC, [yghO] |
| RA | 3,144,041 | C→T | V42I (GTC→ATC) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,171,795 | G→T | A438S (GCG→TCG) | qseC → | sensor histidine kinase QseC |
| RA | 3,243,482 | G→A | T420T (ACC→ACT) | uxaC ← | D‑glucoronate/D‑galacturonate isomerase |
| RA | 3,247,141 | G→A | E164K (GAA→AAA) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,272,462 | G→A | A97V (GCA→GTA) | garR ← | tartronate semialdehyde reductase |
| RA | 3,276,325 | G→A | E348E (GAG→GAA) | garD → | GarD |
| RA | 3,279,461 | A→G | H183R (CAT→CGT) | kbaZ → | putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone |
| RA | 3,293,673 | G→A | E92K (GAA→AAA) | lpoA → | outer membrane lipoprotein ‑ activator of MrcA activity |
| RA | 3,302,892 | G→A | W135* (TGG→TAG) | ubiV → | ubiquinone biosynthesis protein UbiV |
| RA | 3,310,463 | C→A | E236* (GAG→TAG) | pnp ← | polynucleotide phosphorylase |
| RA | 3,336,411 | 2 bp→AT | coding (83‑84/1260 nt) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,342,672 | G→A | E134K (GAA→AAA) | kdsC → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase KdsC |
| RA | 3,342,825 | G→A | G185R (GGG→AGG) | kdsC → | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate phosphatase KdsC |
| RA | 3,360,043 | C→A | F282L (TTC→TTA) | gltD → | glutamate synthase subunit GltD |
| MC JC | 3,362,328 | Δ3,228 bp | IS5‑mediated | [yhcA]–[yhcE] | [yhcA], yhcD, [yhcE] |
| RA | 3,377,372 | G→A | P17S (CCT→TCT) | sspA ← | stringent starvation protein A |
| RA | 3,377,902 | G→A | G102G (GGC→GGT) | rpsI ← | 30S ribosomal subunit protein S9 |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,388,421 | C→T | A236T (GCC→ACC) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,389,971 | C→T | S151F (TCC→TTC) | aaeR → | DNA‑binding transcriptional activator AaeR |
| RA | 3,390,186 | C→T | P223S (CCG→TCG) | aaeR → | DNA‑binding transcriptional activator AaeR |
| RA | 3,392,825 | G→A | T1145I (ACT→ATT) | yhdP ← | phospholipid transport factor YhdP |
| RA | 3,397,720 | C→T | E26K (GAA→AAA) | rng ← | RNase G |
| RA | 3,413,728 | G→A | intergenic (‑263/‑136) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,476,285 | G→A | H52H (CAC→CAT) | yheO ← | DNA‑binding transcriptional regulator YheO |
| RA | 3,515,325 | G→A | H197Y (CAC→TAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,518,683 | G→A | P128S (CCG→TCG) | aroK ← | shikimate kinase 1 |
| RA | 3,522,059 | C→T | E231E (GAG→GAA) | hofM ← | DNA utilization protein HofM |
| RA | 3,539,633 | G→A | G750D (GGT→GAT) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,539,686 | G→A | A768T (GCA→ACA) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,540,703 | G→A | E99E (GAG→GAA) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,653,231 | Δ52,001 bp | IS5‑mediated | yhiS–[dppB] | 43 genes yhiS, slp, dctR, yhiD, hdeB, hdeA, hdeD, arrS, gadE, gadF, mdtE, mdtF, gadW, gadY, gadX, gadA, ccp, treF, yhjB, rcdB, yhjD, yhjE, yhjG, pdeH, kdgK, yhjJ, dctA, pdeK, bcsC, bcsZ, bcsB, bcsA, yhjR, bcsE, bcsF, bcsG, ldrD, rdlD, yhjV, dppF, dppD, dppC, [dppB] |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,708,467 | Δ168 bp | [proK] | [proK] | |
| MC JC | 3,722,076 | Δ15 bp | IS150‑mediated | insK → / ← glyS | IS150 family conserved protein InsB/glycine‑‑tRNA ligase subunit beta |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,781,198 | C→A | intergenic (+181/‑17) | lldD → / → trmL | L‑lactate dehydrogenase/tRNA (cytidine/uridine‑2'‑O)‑ribose methyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,820,207 | C→T | G322S (GGT→AGT) | ligB ← | DNA ligase B |
| JC | 3,822,651 | (CAGGAT)1→2 | coding (252/2109 nt) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,162 | C→T | H255Y (CAC→TAC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,825,407 | C→T | G66G (GGC→GGT) | recG → | ATP‑dependent DNA helicase RecG |
| RA | 3,825,900 | G→A | A231T (GCG→ACG) | recG → | ATP‑dependent DNA helicase RecG |
| RA | 3,828,778 | C→A | intergenic (‑113/‑167) | gltS ← / → xanP | glutamate:sodium symporter/xanthine:H(+) symporter XanP |
| RA | 3,834,118 | C→T | V140V (GTG→GTA) | yicI ← | alpha‑D‑xyloside xylohydrolase |
| RA | 3,838,186 | C→T | intergenic (+49/‑62) | setC → / → yicL | putative arabinose exporter/putative transporter YicL |
| RA | 3,839,040 | C→T | L265L (CTG→TTG) | yicL → | putative transporter YicL |
| RA | 3,839,178 | C→T | W272* (TGG→TGA) | nlpA ← | lipoprotein‑28 |
| RA | 3,840,776 | C→T | V322I (GTT→ATT) | nepI ← | purine ribonucleoside exporter |
| RA | 3,847,493 | C→T | A378T (GCA→ACA) | uhpC ← | inner membrane protein sensing glucose‑6‑phosphate |
| RA | 3,849,109 | C→T | S343N (AGC→AAC) | uhpB ← | sensory histidine kinase UhpB |
| RA | 3,849,393 | C→T | W248* (TGG→TGA) | uhpB ← | sensory histidine kinase UhpB |
| RA | 3,858,628 | C→T | D497N (GAC→AAC) | yidK ← | putative transporter YidK |
| RA | 3,863,026 | C→T | G193D (GGC→GAC) | glvC ← | putative PTS enzyme II component GlvC |
| RA | 3,864,292 | C→T | P132S (CCG→TCG) | yidP → | putative DNA‑binding transcriptional regulator YidP |
| RA | 3,865,138 | C→T | G379E (GGG→GAG) | yidE ← | putative transport protein YidE |
| RA | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| RA | 3,873,018 | C→T | A199T (GCG→ACG) | dgoA ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | 3,876,009 | C→T | S191F (TCC→TTC) | yidX → | putative lipoprotein YidX |
| RA | 3,876,361 | C→T | G198S (GGT→AGT) | yidA ← | sugar phosphatase YidA |
| RA | 3,878,536 | G→A | Y528Y (TAC→TAT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,880,995 | C→T | G76D (GGC→GAC) | recF ← | recombination mediator protein RecF |
| RA | 3,883,568 | C→T | K54K (AAG→AAA) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | 3,890,215 | C→T | intergenic (+70/‑21) | tnaA → / → tnaB | tryptophanase/tryptophan:H(+) symporter TnaB |
| JC JC | 3,890,222 | IS5 (–) +4 bp | intergenic (+77/‑11) | tnaA → / → tnaB | tryptophanase/tryptophan:H(+) symporter TnaB |
| RA | 3,894,704 | C→T | S18L (TCA→TTA) | yieF → | quinone reductase |
| RA | 3,902,608 | C→T | G365D (GGC→GAC) | bglB ← | 6‑phospho‑beta‑glucosidase B |
| RA | 3,904,791 | C→T | W269* (TGG→TGA) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,911,468 | C→T | A20T (GCT→ACT) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,917,210 | C→T | A56T (GCA→ACA) | atpD ← | ATP synthase F1 complex subunit beta |
| RA | 3,919,605 | C→T | G85S (GGC→AGC) | atpA ← | ATP synthase F1 complex subunit alpha |
| RA | 3,920,316 | C→T | D30N (GAC→AAC) | atpH ← | ATP synthase F1 complex subunit delta |
| RA | 3,933,793 | C→T | Q6* (CAG→TAG) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 3,935,212 | C→T | R479C (CGT→TGT) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 3,937,813 | C→T | P174S (CCT→TCT) | rbsK → | ribokinase |
| RA | 3,938,959 | G→A | G245R (GGA→AGA) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,943,540 | C→T | intergenic (+30/‑164) | gltU → / → rrlC | tRNA‑Glu/23S ribosomal RNA |
| RA | 3,943,585 | G→T | intergenic (+75/‑119) | gltU → / → rrlC | tRNA‑Glu/23S ribosomal RNA |
| RA | 3,952,987 | C→T | S168S (TCC→TCT) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 3,996,049 | T→A | L156* (TTG→TAG) | yigA → | DUF484 domain‑containing protein YigA |
| RA | 4,008,757 | C→A | S101S (TCG→TCT) | rhtB ← | L‑homoserine/L‑homoserine lactone/L‑threonine exporter |
| RA | 4,011,802 | C→T | P243S (CCG→TCG) | bioP → | biotin transporter |
| RA | 4,084,903 | T→G | N307T (AAC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,092,703 | A→G | F41L (TTC→CTC) | frvA ← | putative PTS enzyme IIA component FrvA |
| RA | 4,099,498 | G→T | A343E (GCG→GAG) | rhaT ← | rhamnose/lyxose:H(+) symporter |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,159,493 | C→T | G433D (GGC→GAC) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,161,248 | G→T | G61V (GGC→GTC) | fabR → | DNA‑binding transcriptional repressor FabR |
| RA | 4,164,123 | C→G | A162G (GCA→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,178,371 | G→T | intergenic (+83/‑76) | nusG → / → rplK | transcription termination/antitermination factor NusG/50S ribosomal subunit protein L11 |
| RA | 4,184,612 | G→A | G1123D (GGT→GAT) | rpoB → | RNA polymerase subunit beta |
| JC JC | 4,197,558 | IS2 (+) +5 bp | coding (656‑660/774 nt) | nudC → | RNA decapping hydrolase |
| RA | 4,199,747 | G→A | A82T (GCC→ACC) | yjaG → | DUF416 domain‑containing protein YjaG |
| RA | 4,200,155 | (C)6→5 | intergenic (+61/‑126) | yjaG → / → hupA | DUF416 domain‑containing protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,205,310 | G→A | P208S (CCG→TCG) | purD ← | phosphoribosylamine‑‑glycine ligase |
| RA | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,217,172 | G→A | G22S (GGC→AGC) | aceA → | isocitrate lyase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,236,551 | G→A | G97D (GGC→GAC) | yjbF → | lipoprotein YjbF |
| RA | 4,238,103 | G→A | G157D (GGC→GAC) | yjbH → | putative lipoprotein YjbH |
| RA | 4,251,266 | G→A | intergenic (+792/‑1240) | malM → / → ubiC | maltose regulon periplasmic protein/chorismate lyase |
| RA | 4,255,284 | G→A | L395L (CTG→TTG) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,282,332 | (A)5→6 | coding (744/1293 nt) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,351,032 | C→A | G211C (GGC→TGC) | dcuS ← | sensor histidine kinase DcuS |
| JC JC | 4,366,849 | IS4 (+) +12 bp | noncoding (92‑103/113 nt) | aspX ← | small regulatory RNA AspX |
| RA | 4,375,455 | G→T | P68Q (CCG→CAG) | epmB ← | lysine 2,3‑aminomutase |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,429,819 | G→A | intergenic (+264/‑45) | fklB → / → cycA | peptidyl‑prolyl cis‑trans isomerase FklB/D‑serine/alanine/glycine/:H(+)symporter |
| RA | 4,430,212 | G→A | A117T (GCA→ACA) | cycA → | D‑serine/alanine/glycine/:H(+)symporter |
| RA | 4,462,413 | T→C | E83G (GAG→GGG) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| RA | 4,542,517 | G→T | G161W (GGG→TGG) | fimE → | regulator for fimA |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196304 | 1211462 | 15159 | 36 [33] | [34] 36 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1266030 | 1266756 | 727 | 36 [34] | [33] 35 | [prfA]–[prmC] | [prfA],[prmC] |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 112 [0] | [0] 130 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2112201 | 2174816 | 62616 | 100 [0] | [0] 84 | [rfbB]–[gatA] | [rfbB],galF,wcaM,wcaL,wcaK,wzxC,wcaJ,cpsG,cpsB,wcaI,gmm,fcl,gmd,wcaF,wcaE,wcaD,wcaC,wcaB,wcaA,wzc,wzb,wza,yegH,asmA,dcd,udk,dgcE,alkA,yegD,yegI,yegJ,pphC,yegL,sibA,ibsA,sibB,ibsB,mdtA,mdtB,mdtC,mdtD,baeS,baeR,yegP,trhP,cyaR,ogrK,yegR,yegS,gatR,insE5,insF5,gatR,gatD,gatB,[gatA] |
| * | * | ÷ | NC_000913 | 3423857–3424233 | 3424446–3424239 | 7–590 | 35 [34] | [33] 35 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3625589 | 3639754 | 14166 | 115 [0] | [2] 163 | yhhJ–uspB | yhhJ,rbbA,yhiI,yhiY,yhiJ,yhiM,yhiN,pitA,uspB |
| * | * | ÷ | NC_000913 | 4134095 | 4152952 | 18858 | 120 [0] | [0] 138 | [katG]–[ppc] | [katG],yijE,yijF,gldA,fsaB,ptsA,frwC,frwB,pflD,pflC,frwD,yijO,eptC,[ppc] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 112 (1.070) | 72/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 82 (0.790) | 57/598 | 0.5 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 2174817 = | 0 (0.000) | coding (233/453 nt) | gatA | galactitol‑specific PTS enzyme IIA component | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 130 (1.250) | 86/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | = 2112200 | 0 (0.000) | 100 (0.960) | 68/598 | 0.2 | 100% | coding (862/1086 nt) | rfbB | dTDP‑glucose 4,6‑dehydratase 1 |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 3625588 | 0 (0.000) | 112 (1.080) +CCC |
74/592 | 0.1 | 100% | intergenic (+74/+91) | yhhI/yhhJ | putative transposase/ABC transporter family protein YhhJ |
| ? | NC_000913 | 3720633 = | NA (NA) | noncoding (1/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 3639755 = | 0 (0.000) | 160 (1.540) | 89/594 | 0.0 | 100% | intergenic (‑35/‑356) | uspB/uspA | universal stress protein B/universal stress protein A |
| ? | NC_000913 | = 3722075 | NA (NA) | noncoding (1443/1443 nt) | IS150 | repeat region | |||||
| * | ? | NC_000913 | 3720633 = | NA (NA) | 138 (1.340) | 87/592 | 0.0 | 100% | noncoding (1/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 4152953 = | 0 (0.000) | coding (146/2652 nt) | ppc | phosphoenolpyruvate carboxylase | |||||
| * | ? | NC_000913 | = 3722075 | NA (NA) | 119 (1.140) | 79/598 | 0.1 | 100% | noncoding (1443/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 4134094 | 0 (0.000) | coding (260/2181 nt) | katG | catalase/hydroperoxidase HPI | |||||
| * | ? | NC_000913 | 4542682 = | 55 (0.530) | 116 (1.150) | 64/580 | 0.2 | 69.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 49 (0.480) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 64 (0.610) | 109 (1.080) | 76/580 | 0.1 | 66.2% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 49 (0.480) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||