mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 75,677 | A→C | 100% | F541L (TTT→TTG) | sgrR ← | DNA‑binding transcriptional regulator |
| RA | 118,976 | G→A | 12.2% | G82S (GGT→AGT) | ampD → | N‑acetyl‑anhydromuranmyl‑L‑alanine amidase |
| RA | 121,347 | T→C | 70.0% | M69V (ATG→GTG) | aroP ← | aromatic amino acid transporter |
| RA | 155,463 | A→T | 100% | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 162,916 | C→T | 55.6% | A271V (GCG→GTG) | hrpB → | predicted ATP‑dependent helicase |
| RA | 199,072 | T→C | 16.0% | V382A (GTC→GCC) | yaeT → | conserved hypothetical protein |
| RA | 237,726 | A→G | 14.9% | N131S (AAC→AGC) | yafT → | predicted aminopeptidase |
| RA | 286,496 | T→C | 35.3% | F162L (TTT→CTT) | yagH → | predicted xylosidase/arabinosidase |
| RA | 330,966 | T→G | 68.3% | intergenic (+246/‑629) | betT → / → yahA | choline transporter of high affinity/predicted DNA‑binding transcriptional regulator |
| RA | 376,160 | G→T | 100% | Q55H (CAG→CAT) | yaiL → | nucleoprotein/polynucleotide‑associated enzyme |
| RA | 488,806 | Δ1 bp | 100% | coding (3047/3363 nt) | kefA → | fused mechanosensitive channel proteins |
| RA | 505,179 | C→T | 100% | L348L (CTG→TTG) | ushA → | bifunctional UDP‑sugar hydrolase and 5'‑nucleotidase |
| RA | 540,085 | C→T | 12.9% | I99I (ATC→ATT) | ybbY → | predicted uracil/xanthine transporter |
| RA | 547,694 | A→G | 100% | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,831:1 | +G | 100% | pseudogene (251/261 nt) pseudogene (251/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 582,879 | G→A | 11.3% | intergenic (+596/‑25) | ylcE → / → appY | hypothetical protein/DNA‑binding transcriptional activator |
| MC JC | 654,214 | Δ1,199 bp | 100% | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 686,526 | A→G | 66.7% | I189T (ATC→ACC) | gltJ ← | glutamate and aspartate transporter subunit |
| RA | 707,271 | C→T | 14.2% | H253Y (CAC→TAC) | glnS → | glutamyl‑tRNA synthetase |
| RA | 710,341 | C→T | 68.0% | P44S (CCA→TCA) | ybfN → | predicted lipoprotein |
| RA | 712,019 | G→A | 79.0% | intergenic (‑132/+8) | fldA ← / ← ybfE | flavodoxin 1/LexA regulated protein |
| RA | 767,363 | T→C | 62.5% | L320L (TTG→CTG) | mngA → | fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzyme IIABC components |
| RA | 847,104 | A→G | 86.2% | R146R (CGT→CGC) | glnP ← | glutamine transporter subunit |
| RA | 884,617 | G→A | 79.0% | V175I (GTT→ATT) | cmr → | multidrug efflux system protein |
| RA | 894,963 | A→C | 14.6% | N253T (AAC→ACC) | potF → | putrescine transporter subunit |
| RA | 905,152 | Δ1 bp | 100% | coding (138/324 nt) | ybjQ → | conserved hypothetical protein |
| RA | 940,557 | A→G | 78.0% | P236P (CCA→CCG) | serS → | seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine |
| RA | 1,006,848 | A→T | 100% | K159* (AAA→TAA) | ycbW → | hypothetical protein |
| RA | 1,051,238 | T→C | 74.1% | intergenic (+286/+147) | insB → / ← cspH | IS1 transposase InsAB'/stress protein, member of the CspA‑family |
| RA | 1,068,568 | T→A | 78.0% | G22G (GGT→GGA) | ymdF → | conserved hypothetical protein |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,110,226 | G→T | 15.1% | A98D (GCC→GAC) | mdoC ← | membrane protein required for modification of periplasmic glucan |
| RA | 1,135,828 | T→C | 71.4% | D150D (GAT→GAC) | flgF → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,150,273 | A→G | 100% | intergenic (+5/‑63) | plsX → / → fabH | fatty acid/phospholipid synthesis protein/3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,189,339 | A→G | 100% | L160S (TTA→TCA) | ycfD ← | conserved hypothetical protein |
| RA | 1,197,638 | G→A | 67.6% | L313L (CTG→CTA) | icd → | isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,202,265 | G→T | 34.1% | A40D (GCT→GAT) | intE ← | predicted integrase |
| RA | 1,207,066 | A→G | 69.2% | E440E (GAA→GAG) | ymfN → | predicted DNA‑binding transcriptional regulator |
| RA | 1,225,448 | G→A | 57.9% | P59P (CCG→CCA) | ycgI → | hypothetical protein |
| RA | 1,235,640:1 | +A | 53.8% | coding (655/1542 nt) | nhaB ← | sodium:proton antiporter |
| RA | 1,237,778 | C→T | 86.7% | R347R (CGG→CGA) | ycgB ← | conserved hypothetical protein |
| RA | 1,249,660 | A→C | 100% | Y344* (TAT→TAG) | dhaH ← | fused predicted dihydroxyacetone‑specific PTS enzyme HPr component and EI component |
| RA | 1,265,644 | C→T | 52.9% | L118L (CTC→CTT) | hemA → | glutamyl tRNA reductase |
| RA | 1,274,654 | T→C | 100% | S198P (TCA→CCA) | chaC → | regulatory protein for cation transport |
| RA | 1,275,296 | A→G | 73.3% | intergenic (‑120/‑206) | ychN ← / → ychP | conserved hypothetical protein/predicted invasin |
| RA | 1,282,409 | A→G | 81.3% | P323P (CCA→CCG) | narG → | nitrate reductase 1, alpha subunit |
| MC JC | 1,301,041 | Δ1,336 bp | 100% | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | 100% | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,346,872 | C→T | 41.9% | V529I (GTT→ATT) | gmr ← | modulator of Rnase II stability |
| RA | 1,352,814 | G→A | 75.0% | intergenic (‑61/+307) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
| RA | 1,427,357 | A→T | 19.0% | D8V (GAT→GTT) | ydaY → | hypothetical protein |
| RA | 1,427,990 | G→A | 9.1% | intergenic (+296/‑178) | ydaY → / → ynaA | hypothetical protein/predicted tail protein |
| RA | 1,475,513 | A→G | 100% | pseudogene (8408/8622 nt) pseudogene (3110/3324 nt) |
ydbA → ydbA → |
ECK1398:JW5802+JW1402:b4492; predicted outer membrane protein ECK1398:JW1402:b1405; predicted outer membrane protein, C‑ter fragment |
| RA | 1,482,053 | A→G | 100% | D401G (GAT→GGT) | ynbC → | predicted hydrolase |
| RA | 1,484,096 | A→C | 100% | F160C (TTC→TGC) | azoR ← | NADH‑azoreductase, FMN‑dependent |
| RA | 1,489,255 | G→A | 12.1% | A103T (GCG→ACG) | ydcF → | conserved hypothetical protein |
| RA | 1,496,286 | A→G | 69.6% | L167P (CTT→CCT) | ydcI ← | predicted DNA‑binding transcriptional regulator |
| RA | 1,507,250 | A→G | 25.6% | I182T (ATC→ACC) | ydcO ← | predicted benzoate transporter |
| RA | 1,533,715 | T→C | 100% | G62G (GGT→GGC) | ydcC → | conserved hypothetical protein |
| RA | 1,538,270 | A→G | 69.2% | F21S (TTT→TCT) | narV ← | nitrate reductase 2 (NRZ), gamma subunit |
| RA | 1,557,824 | C→T | 22.8% | Q57Q (CAG→CAA) | bdm ← | biofilm‑dependent modulation protein |
| RA | 1,575,785 | C→T | 40.0% | A378T (GCT→ACT) | pqqL ← | predicted peptidase |
| RA | 1,608,013 | G→A | 42.9% | G67E (GGA→GAA) | lsrF → | predicted aldolase |
| RA | 1,609,975 | C→T | 68.8% | L254L (CTG→CTA) | yneE ← | conserved inner membrane protein |
| RA | 1,621,163 | A→G | 12.9% | Q110Q (CAA→CAG) | marR → | DNA‑binding transcriptional repressor |
| RA | 1,642,131 | A→G | 73.0% | Y57H (TAT→CAT) | essQ ← | predicted S lysis protein |
| RA | 1,649,687 | T→C | 19.3% | Y14H (TAT→CAT) | dicA → | predicted regulator for DicB |
| RA | 1,695,171 | T→C | 57.1% | V269V (GTA→GTG) | uidB ← | glucuronide transporter |
| RA | 1,720,894:1 | +C | 100% | coding (423/1110 nt) | ydhH ← | conserved hypothetical protein |
| RA | 1,799,263 | G→A | 31.4% | S132S (AGC→AGT) | pheT ← | phenylalanine tRNA synthetase, beta subunit |
| RA | 1,806,448 | T→C | 58.8% | pseudogene (1641/1900 nt) pseudogene (1157/1416 nt) |
arpB → arpB → |
ECK1718:JW5278+JW1710:b4494; hypothetical protein ECK1718:JW1710:b1721; hypothetical protein, C‑ter fragment |
| RA | 1,807,728 | C→T | 43.7% | A24T (GCT→ACT) | ydiY ← | conserved hypothetical protein |
| RA | 1,810,661 | A→G | 73.0% | F96S (TTT→TCT) | yniB ← | predicted inner membrane protein |
| RA | 1,824,257 | T→C | 13.3% | F29S (TTT→TCT) | nadE → | NAD synthetase, NH3/glutamine‑dependent |
| RA | 1,832,787 | T→C | 21.6% | M304V (ATG→GTG) | astC ← | succinylornithine transaminase, PLP‑dependent |
| RA | 1,837,528 | G→A | 100% | V100V (GTG→GTA) | ynjA → | conserved hypothetical protein |
| RA | 1,865,587 | T→C | 100% | L8L (CTT→CTC) | yeaD → | conserved hypothetical protein |
| RA | 1,873,346 | C→T | 32.2% | L416L (CTC→CTT) | yeaI → | predicted diguanylate cyclase |
| RA | 1,919,937:1 | +C | 81.8% | coding (714/2634 nt) | yebT → | conserved hypothetical protein |
| RA | 1,990,800 | A→G | 100% | intergenic (+118/‑53) | yecR → / → ftn | hypothetical protein/cytoplasmic ferritin iron storage protein |
| RA | 2,000,742 | C→T | 58.1% | M292I (ATG→ATA) | yedO ← | D‑cysteine desulfhydrase, PLP‑dependent |
| RA | 2,002,183 | G→A | 15.2% | R114C (CGC→TGC) | fliY ← | cystine transporter subunit |
| RA | 2,027,468 | Δ1 bp | 100% | intergenic (+118/‑180) | yodD → / → yedP | hypothetical protein/conserved hypothetical protein |
| RA | 2,039,900 | A→G | 32.6% | I130I (ATT→ATC) | yedV ← | predicted sensory kinase in two‑component regulatory system with YedW |
| RA | 2,041,745 | C→T | 100% | A44V (GCC→GTC) | yedY → | predicted reductase |
| RA | 2,065,027 | G→T | 55.8% | A145D (GCT→GAT) | erfK ← | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,075,214 | C→T | 49.1% | N513N (AAC→AAT) | flu → | antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,077,011 | G→A | 44.1% | L32L (CTG→CTA) | yeeR → | predicted membrane protein |
| RA | 2,081,459 | A→G | 10.8% | F36L (TTT→CTT) | yeeX ← | conserved hypothetical protein |
| RA | 2,096,084 | G→A | 87.5% | E160E (GAG→GAA) | hisB → | fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase |
| RA | 2,117,348 | C→T | 18.2% | G229D (GGC→GAC) | wcaM ← | predicted colanic acid biosynthesis protein |
| RA | 2,143,096 | C→T | 12.9% | A218A (GCG→GCA) | asmA ← | predicted assembly protein |
| RA | 2,144,746 | C→T | 18.4% | V114I (GTC→ATC) | udk ← | uridine/cytidine kinase |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,178,242 | G→A | 10.6% | P48S (CCT→TCT) | gatA ← | galactitol‑specific enzyme IIA component of PTS |
| RA | 2,213,335 | A→G | 10.6% | N301S (AAT→AGT) | yehQ → | hypothetical protein |
| RA | 2,215,186 | A→G | 69.0% | V115V (GTT→GTC) | yehS ← | conserved hypothetical protein |
| RA | 2,237,502 | A→G | 66.7% | K46E (AAA→GAA) | yeiT → | predicted oxidoreductase |
| RA | 2,257,455 | C→T | 74.0% | G9R (GGA→AGA) | yeiJ ← | predicted nucleoside transporter |
| RA | 2,268,596 | T→C | 50.0% | T12A (ACT→GCT) | yeiW ← | conserved hypothetical protein |
| RA | 2,271,945 | A→G | 42.5% | R261R (CGA→CGG) | yeiR → | hypothetical protein |
| RA | 2,274,249 | A→G | 100% | T64A (ACT→GCT) | rtn → | conserved hypothetical protein |
| RA | 2,291,258 | C→T | 9.2% | G326D (GGC→GAC) | yejO ← | predicted autotransporter outer membrane protein |
| RA | 2,295,693 | C→T | 100% | A18T (GCG→ACG) | ccmH ← | heme lyase, CcmH subunit |
| RA | 2,298,568 | T→C | 32.0% | E49E (GAA→GAG) | ccmE ← | periplasmic heme chaperone |
| RA | 2,307,310 | C→T | 77.8% | V24V (GTC→GTT) | eco → | ecotin, a serine protease inhibitor |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,335,995 | C→T | 21.9% | pseudogene (3078/4605 nt) pseudogene (3078/4104 nt) |
yfaS ← yfaS ← |
ECK2220:JW2222+JW2221:b4500; hypothetical protein ECK2220:JW2222:b2228; hypothetical protein, N‑ter fragment |
| RA | 2,345,374 | C→T | 24.3% | G1156S (GGT→AGT) | yfaL ← | adhesin |
| RA | 2,387,662 | T→C | 47.4% | Y94H (TAT→CAT) | elaD → | hypothetical protein |
| RA | 2,426,403 | G→A | 70.4% | G113R (GGG→AGG) | yfcG → | predicted glutathione S‑transferase |
| RA | 2,440,837 | C→T | 64.5% | A82A (GCG→GCA) | truA ← | pseudouridylate synthase I |
| RA | 2,452,377 | C→T | 72.0% | P181P (CCG→CCA) | aroC ← | chorismate synthase |
| RA | 2,469,991 | T→C | 32.8% | S155G (AGC→GGC) | vacJ ← | predicted lipoprotein |
| RA | 2,512,230 | A→G | 100% | W371R (TGG→CGG) | ypdG ← | predicted enzyme IIC component of PTS |
| RA | 2,559,548 | T→C | 60.7% | I293T (ATT→ACT) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,560,022 | G→A | 58.3% | P203S (CCT→TCT) | yfeG ← | predicted DNA‑binding transcriptional regulator |
| RA | 2,611,108 | T→C | 8.3% | F185L (TTC→CTC) | hyfR → | DNA‑binding transcriptional activator, formate sensing |
| RA | 2,620,788 | A→G | 62.5% | E312E (GAA→GAG) | purM → | phosphoribosylaminoimidazole synthetase |
| RA | 2,629,792 | T→C | 10.7% | D467G (GAC→GGC) | guaA ← | GMP synthetase |
| RA | 2,632,142 | C→T | 22.7% | M195I (ATG→ATA) | guaB ← | IMP dehydrogenase |
| RA | 2,646,699 | C→G | 73.9% | Q1415H (CAG→CAC) | yfhM ← | conserved hypothetical protein |
| RA | 2,732,756 | T→A | 65.8% | D25V (GAC→GTC) | clpB ← | protein disaggregation chaperone |
| RA | 2,750,169 | C→T | 12.0% | T228M (ACG→ATG) | yfjB → | NAD kinase |
| RA | 2,770,406 | T→C | 35.3% | intergenic (+135/+90) | yfjT → / ← yfjU | hypothetical protein/conserved hypothetical protein |
| RA | 2,809,581 | G→A | 9.5% | G52G (GGG→GGA) | mprA → | DNA‑binding transcriptional regulator |
| RA | 2,841,701 | C→T | 48.8% | L134L (CTG→CTA) | hycH ← | protein required for maturation of hydrogenase 3 |
| RA | 2,863,108 | T→C | 19.4% | L73L (TTA→CTA) | ygbM → | conserved hypothetical protein |
| RA | 2,866,110 | T→A | 100% | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,866,848:1 | +T | 40.7% | coding (562/1140 nt) | nlpD ← | predicted outer membrane lipoprotein |
| RA | 2,875,612 | G→A | 64.1% | D126N (GAT→AAT) | iap → | aminopeptidase in alkaline phosphatase isozyme conversion |
| RA | 2,894,340 | C→T | 73.7% | W32* (TGG→TGA) | ygcQ ← | predicted flavoprotein |
| RA | 2,902,330 | A→T | 15.4% | intergenic (+300/+1073) | ygcE → / ← ygcF | predicted kinase/conserved hypothetical protein |
| RA | 2,927,326 | G→A | 75.0% | V148M (GTG→ATG) | sdaC → | predicted serine transporter |
| RA | 2,960,928 | T→C | 51.3% | K53E (AAG→GAG) | recC ← | exonuclease V (RecBCD complex), gamma chain |
| RA | 2,968,686 | A→G | 100% | I123M (ATA→ATG) | mutH → | methyl‑directed mismatch repair protein |
| RA | 2,971,401 | A→T | 56.2% | V373E (GTG→GAG) | ygeD ← | predicted inner membrane protein |
| RA | 2,976,020 | C→T | 59.4% | L256F (CTC→TTC) | galR → | DNA‑binding transcriptional repressor |
| RA | 2,983,818 | A→G | 9.8% | V144A (GTG→GCG) | yqeF ← | predicted acyltransferase |
| RA | 2,989,682 | C→T | 7.7% | intergenic (+26/‑242) | ygeF → / → ygeG | hypothetical protein/predicted chaperone |
| RA | 2,989,906 | A→G | 8.1% | intergenic (+250/‑18) | ygeF → / → ygeG | hypothetical protein/predicted chaperone |
| RA | 2,993,568 | C→A | 16.6% | intergenic (‑9/+25) | ygeK ← / ← ygeL | predicted DNA‑binding transcriptional regulator/hypothetical protein |
| RA | 3,018,630 | G→A | 40.0% | D272N (GAC→AAC) | ssnA → | predicted chlorohydrolase/aminohydrolase |
| RA | 3,065,306 | A→G | 73.5% | V175A (GTT→GCT) | ygfI ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,100,981 | A→G | 15.6% | H176H (CAT→CAC) | yggH ← | tRNA (m7G46) methyltransferase, SAM‑dependent |
| RA | 3,140,619 | C→T | 12.1% | A343T (GCA→ACA) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,141,409 | C→T | 9.7% | A79A (GCG→GCA) | hybC ← | hydrogenase 2, large subunit |
| RA | 3,179,239 | C→T | 73.7% | L55L (CTG→TTG) | ygiC → | hypothetical protein |
| RA | 3,193,337 | C→A | 44.4% | intergenic (+156/+639) | yqiK → / ← rfaE | conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| RA | 3,204,990 | T→C | 13.0% | intergenic (‑78/‑129) | ygiP ← / → ttdA | predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit |
| RA | 3,211,677 | C→T | 9.4% | intergenic (+169/‑26) | dnaG → / → rpoD | DNA primase/RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,222,206 | C→T | 78.1% | N306N (AAC→AAT) | ebgA → | cryptic beta‑D‑galactosidase, alpha subunit |
| RA | 3,232,470 | A→G | 79.0% | L111L (TTG→CTG) | ygjM ← | predicted DNA‑binding transcriptional regulator |
| RA | 3,272,348 | C→T | 10.4% | G89S (GGT→AGT) | garR ← | tartronate semialdehyde reductase |
| RA | 3,277,106 | A→G | 70.4% | T84A (ACT→GCT) | sohA → | predicted regulator |
| RA | 3,291,041 | A→G | 50.9% | L791L (CTA→CTG) | yraJ → | predicted outer membrane protein |
| RA | 3,328,359 | T→C | 14.7% | N71S (AAC→AGC) | greA ← | transcription elongation factor |
| RA | 3,343,341 | T→C | 80.9% | I36T (ATC→ACC) | yhbN → | predicted transporter subunit |
| RA | 3,348,085 | G→A | 25.6% | E89K (GAA→AAA) | npr → | phosphohistidinoprotein‑hexose phosphotransferase component of N‑regulated PTS system (Npr) |
| RA | 3,351,511 | A→G | 36.1% | V457A (GTG→GCG) | arcB ← | hybrid sensory histidine kinase in two‑component regulatory system with ArcA |
| RA | 3,374,409 | A→G | 56.3% | intergenic (‑65/‑315) | nanR ← / → dcuD | DNA‑binding transcriptional dual regulator/predicted transporter |
| RA | 3,404,628 | A→C | 18.6% | intergenic (+315/‑663) | yhdH → / → accB | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit |
| RA | 3,404,742 | G→A | 83.5% | intergenic (+429/‑549) | yhdH → / → accB | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding/acetyl CoA carboxylase, BCCP subunit |
| RA | 3,442,070 | A→G | 70.3% | T497A (ACG→GCG) | thiC → | thiamin (pyrimidine moiety) biosynthesis protein |
| RA | 3,473,895 | A→G | 71.4% | E162G (GAG→GGG) | trmA → | tRNA (uracil‑5‑)‑methyltransferase |
| RA | 3,488,502 | C→T | 15.2% | L47L (CTG→TTG) | yijO → | predicted DNA‑binding transcriptional regulator |
| RA | 3,497,705 | T→G | 76.4% | R20R (CGT→CGG) | gldA → | glycerol dehydrogenase, NAD |
| RA | 3,500,231 | C→T | 85.3% | A115T (GCG→ACG) | yijE ← | predicted permease |
| RA | 3,504,714 | G→A | 100% | F711F (TTC→TTT) | metL ← | fused aspartokinase II and homoserine dehydrogenase II |
| RA | 3,560,351 | G→A | 16.4% | P62L (CCC→CTC) | rbn ← | tRNA processing exoribonuclease BN |
| RA | 3,560,998 | A→G | 13.9% | F44S (TTT→TCT) | yihX ← | predicted hydrolase |
| RA | 3,572,896 | C→T | 33.3% | R171* (CGA→TGA) | ompL → | predicted outer membrane porin L |
| RA | 3,582,634 | A→G | 100% | D411G (GAC→GGC) | glnG → | fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
| RA | 3,587,844 | T→C | 68.2% | P624P (CCA→CCG) | polA ← | fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
| RA | 3,591,039 | G→A | 25.0% | intergenic (+28/+13) | yihG → / ← yihF | predicted endonuclease/conserved hypothetical protein |
| RA | 3,591,880 | C→T | 10.4% | M201I (ATG→ATA) | yihF ← | conserved hypothetical protein |
| RA | 3,594,183 | A→G | 61.1% | D28D (GAT→GAC) | yihE ← | predicted kinase |
| RA | 3,602,757 | T→A | 8.1% | L260F (TTA→TTT) | trkH ← | potassium transporter |
| RA | 3,614,917 | G→A | 52.1% | G513G (GGC→GGT) | ubiB ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,626,383 | C→T | 12.1% | A33A (GCG→GCA) | yigL ← | predicted hydrolase |
| RA | 3,671,661 | G→A | 15.9% | R204Q (CGG→CAG) | rhlB → | ATP‑dependent RNA helicase |
| RA | 3,701,075 | T→C | 13.5% | L107L (TTA→TTG) | rbsC ← | D‑ribose transporter subunit |
| RA | 3,712,033 | G→A | 13.6% | M328I (ATG→ATA) | gidA → | glucose‑inhibited cell‑division protein |
| RA | 3,714,423 | C→T | 100% | H61Y (CAC→TAC) | atpI → | ATP synthase, membrane‑bound accesory subunit |
| RA | 3,718,376 | G→A | 10.2% | intergenic (+9/‑42) | atpA → / → atpG | F1 sector of membrane‑bound ATP synthase, alpha subunit/F1 sector of membrane‑bound ATP synthase, gamma subunit |
| MC JC | 3,742,938 | Δ1,336 bp | 100% | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | 100% | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | 100% | insH | insH | |
| RA | 3,767,300 | A→G | 55.6% | I166V (ATA→GTA) | dgoA → | 2‑oxo‑3‑deoxygalactonate 6‑phosphate aldolase |
| RA | 3,769,914 | G→A | 75.6% | A410T (GCC→ACC) | dgoT → | D‑galactonate transporter |
| RA | 3,777,889 | T→C | 51.4% | V359A (GTG→GCG) | glvC → | arbutin specific enzyme IIC component of PTS |
| RA | 3,824,280 | T→C | 100% | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | 100% | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | 100% | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | 100% | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | 100% | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | 100% | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | 100% | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | 100% | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | 100% | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,533:1 | +G | 100% | pseudogene (666/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,903,549 | T→C | 10.9% | S104P (TCA→CCA) | bax → | conserved hypothetical protein |
| RA | 3,918,430 | G→A | 8.0% | L264L (CTG→TTG) | insK ← | IS150 conserved protein InsB |
| RA | 3,958,682 | C→T | 12.2% | A69V (GCC→GTC) | yhjJ → | predicted zinc‑dependent peptidase |
| RA | 3,998,196 | A→G | 13.2% | Y454H (TAT→CAT) | yhiP ← | predicted transporter |
| RA | 4,000,806 | A→T | 7.8% | D37V (GAT→GTT) | yhiO → | predicted universal stress (ethanol tolerance) protein B |
| RA | 4,007,539 | G→A | 81.6% | pseudogene (367/393 nt) | yhiK → | ECK3474:JW5674:b3489; hypothetical protein |
| RA | 4,013,034 | C→T | 12.2% | P719L (CCG→CTG) | rbbA → | fused ribosome‑associated ATPases |
| RA | 4,042,971 | G→A | 85.2% | A39T (GCC→ACC) | livK → | leucine transporter subunit |
| RA | 4,057,014 | A→G | 11.4% | I121I (ATT→ATC) | yrhA ← | conserved hypothetical protein |
| RA | 4,064,053 | T→A | 39.9% | I233N (ATC→AAC) | gntU → | gluconate transporter, low affinity GNT 1 system |
| RA | 4,099,912 | C→T | 86.3% | A34T (GCT→ACT) | feoB ← | fused ferrous iron transporter, protein B |
| RA | 4,103,846 | T→C | 86.5% | Y5H (TAC→CAC) | ompR → | DNA‑binding response regulator in two‑component regulatory system with EnvZ |
| RA | 4,125,813 | C→T | 15.8% | P152L (CCT→CTT) | rpe → | D‑ribulose‑5‑phosphate 3‑epimerase |
| RA | 4,184,035 | C→A | 84.6% | G3* (GGA→TGA) R269M (AGG→ATG) |
gspD ← gspC ← |
general secretory pathway component, cryptic general secretory pathway component, cryptic |
| RA | 4,208,832 | A→G | 13.6% | H126R (CAC→CGC) | yrdD → | predicted DNA topoisomerase |
| RA | 4,225,730 | G→A | 11.8% | T117I (ACT→ATT) | arpA ← | regulator of acetyl CoA synthetase |
| RA | 4,245,658 | G→A | 47.6% | S63S (AGC→AGT) | xylE ← | D‑xylose transporter |
| MC JC | 4,310,365 | Δ1,199 bp | 100% | insH–[alsK] | insH, [alsK] | |
| RA | 4,354,061 | C→T | 15.9% | G218G (GGG→GGA) | dcuR ← | DNA‑binding response regulator in two‑component regulatory system with DcuS |
| RA | 4,361,585 | C→T | 17.1% | P571P (CCG→CCA) | cadA ← | lysine decarboxylase 1 |
| RA | 4,362,267 | T→G | 15.2% | E344A (GAA→GCA) | cadA ← | lysine decarboxylase 1 |
| RA | 4,371,273 | Δ2 bp | 100% | intergenic (‑6/+299) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,405,345 | G→A | 17.8% | intergenic (+67/‑9) | hfq → / → hflX | HF‑I, host factor for RNA phage Q beta replication/predicted GTPase |
| RA | 4,431,950 | A→G | 76.9% | V52A (GTT→GCT) | yjfZ ← | hypothetical protein |
| RA | 4,495,142 | C→T | 6.3% | G227E (GGA→GAA) | idnR ← | DNA‑binding transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,527,342 | C→T | 10.6% | E479K (GAG→AAG) | yjhG ← | predicted dehydratase |
| RA | 4,544,610 | T→C | 8.2% | intergenic (‑427/‑1029) | yjhA ← / → fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,546,724 | T→C | 12.8% | S2S (AGT→AGC) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,547,129 | G→A | 87.8% | M137I (ATG→ATA) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,549,752 | C→T | 19.2% | intergenic (+41/‑26) | fimC → / → fimD | chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis |
| RA | 4,549,754 | G→A | 80.8% | intergenic (+43/‑24) | fimC → / → fimD | chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis |
| RA | 4,558,086 | G→A | 58.1% | A168A (GCG→GCA) | uxuB → | D‑mannonate oxidoreductase, NAD‑binding |
| RA | 4,563,589 | T→A | 100% | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,591,162 | C→A | 75.0% | V112V (GTG→GTT) | hsdR ← | endonuclease R |
| RA | 4,616,051 | T→C | 11.3% | intergenic (+366/‑27) | prfC → / → osmY | peptide chain release factor RF‑3/periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 164568 | 164583 | 16 | 4 [2] | [2] 4 | hrpB/mrcB | predicted ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | * | ÷ | W3110S.gb | 171662 | 171688 | 27 | 4 [2] | [2] 3 | fhuB | fused subunits of iron‑hydroxamate transporter and membrane components of ABC superfamily transporter |
| * | * | ÷ | W3110S.gb | 283099 | 283206 | 108 | 4 [2] | [2] 3 | yagF | predicted dehydratase |
| * | * | ÷ | W3110S.gb | 379239 | 379247 | 9 | 3 [2] | [1] 3 | frmR/yaiO | regulator protein that represses frmRAB operon/hypothetical protein |
| * | * | ÷ | W3110S.gb | 422758 | 422786 | 29 | 4 [2] | [2] 3 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 573872–575008 | 575999 | 992–2128 | 3 [2] | [0] 86 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 598786 | 598800 | 15 | 3 [2] | [0] 6 | cusA | copper/silver efflux system, membrane component |
| * | * | ÷ | W3110S.gb | 721523 | 721551 | 29 | 3 [2] | [0] 3 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 1081320 | 1081346 | 27 | 3 [2] | [1] 3 | putP/ycdN | proline:sodium symporter/ECK1007:JW5141:b1016; hypothetical protein, N‑ter fragment |
| * | * | ÷ | W3110S.gb | 1173181 | 1173215 | 35 | 3 [2] | [2] 4 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1421298 | 1421325 | 28 | 3 [2] | [1] 4 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1928946 | 1928970 | 25 | 3 [2] | [2] 4 | ptrB | protease II |
| * | * | ÷ | W3110S.gb | 2041782 | 2041815 | 34 | 3 [1] | [2] 4 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2296383 | 2296401 | 19 | 4 [2] | [2] 3 | ccmF | heme lyase, CcmF subunit |
| * | * | ÷ | W3110S.gb | 2569112 | 2569141 | 30 | 3 [2] | [2] 4 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2876792 | 2876852 | 61 | 4 [2] | [2] 3 | iap/ygbF | aminopeptidase in alkaline phosphatase isozyme conversion/hypothetical protein |
| * | * | ÷ | W3110S.gb | 3799042 | 3799072 | 31 | 3 [1] | [2] 3 | yicM | predicted transporter |
| * | * | ÷ | W3110S.gb | 3859266 | 3859294 | 29 | 3 [1] | [2] 6 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 4213633–4215889 | 4216703–4215891 | 3–3071 | 3 [1] | [2] 3 | rrlE–[rrfE] | rrlE,[rrfE] |
| * | * | ÷ | W3110S.gb | 4329954 | 4329967 | 14 | 3 [2] | [2] 3 | phnC/phnB | phosphonate/organophosphate ester transporter subunit/conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 4401131 | 4401181 | 51 | 3 [2] | [2] 3 | amiB | N‑acetylmuramoyl‑l‑alanine amidase II |
| * | * | ÷ | W3110S.gb | 4547669 | 4547677 | 9 | 25 [0] | [0] 31 | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| * | * | ÷ | W3110S.gb | 4565150 | 4565176 | 27 | 3 [2] | [2] 3 | yjiH | conserved inner membrane protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 29 (0.990) | 13/100 | NT | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 19 (0.650) | 39 (1.410) +TCA |
23/94 | NT | 81.4% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | 314453 = | 19 (0.650) | 25 (0.890) +TC |
16/96 | NT | 73.3% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 0 (0.000) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 46 (1.570) | 24/100 | NT | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 48 (1.630) | 30/100 | NT | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | = 713954 | 37 (1.260) | 4 (0.140) | 3/100 | NT | 9.9% | coding (546/546 nt) | seqA | regulatory protein for replication initiation |
| ? | W3110S.gb | 2809398 = | 36 (1.230) | intergenic (+63/‑28) | ygaH/mprA | predicted inner membrane protein/DNA‑binding transcriptional regulator | |||||
| * | ? | W3110S.gb | 1209367 = | 12 (0.410) | 19 (0.950) | 14/68 | NT | 65.3% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 12 (0.600) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 13 (0.440) | 8 (0.400) | 6/68 | NT | 43.4% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 12 (0.600) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 0 (0.000) | 16 (0.580) | 10/94 | NT | 100% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 2 (0.070) | 28 (0.990) | 17/96 | NT | 93.6% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 33 (1.150) | 21/98 | NT | 100% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 0 (0.000) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2173565 | NA (NA) | 23 (0.780) | 14/100 | NT | 100% | pseudogene (306/2041 nt) pseudogene (306/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | = 3932933 | 0 (0.000) | coding (222/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 35 (1.190) | 21/100 | NT | 97.2% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 1 (0.030) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | = 3261133 | 0 (0.000) | 26 (0.960) | 16/92 | NT | 100% | intergenic (‑59/‑69) | tdcE/insH | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase/IS5 element protein |
| ? | W3110S.gb | 3262333 = | 0 (0.000) | coding (1183/1296 nt) | tdcD | propionate kinase/acetate kinase C, anaerobic | |||||
| * | ? | W3110S.gb | 3748799 = | 5 (0.170) | 67 (2.280) | 32/100 | NT | 93.1% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | 4547364 = | 1 (0.030) | 22 (0.910) | 14/82 | NT | 98.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | 4547678 = | 0 (0.000) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||
| * | ? | W3110S.gb | = 4547372 | 0 (0.000) | 14 (0.580) | 11/82 | NT | 100% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 0 (0.000) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||