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 | 33,406 | G→C | 5.5% | V864L (GTG→CTG) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 35,739 | C→A | 7.4% | G142C (GGT→TGT) | caiD ← | carnitinyl‑CoA dehydratase |
| RA | 161,068 | A→C | 32.2% | intergenic (+47/‑149) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 221,420 | A→G | 5.1% | noncoding (1163/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,425 | T→C | 7.3% | noncoding (1168/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,430 | T→C | 7.5% | noncoding (1173/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,455 | G→A | 7.5% | noncoding (1198/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,464 | G→C | 7.1% | noncoding (1207/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,471 | C→T | 8.5% | noncoding (1214/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 221,476 | A→T | 8.2% | noncoding (1219/1542 nt) | rrsH → | 16S ribosomal RNA of rrnH operon |
| RA | 223,456 | T→C | 7.5% | noncoding (1211/2904 nt) | rrlH → | 23S ribosomal RNA of rrnH operon |
| RA | 235,769 | G→T | 6.1% | pseudogene (177/273 nt) | yafF → | pseudogene, H repeat‑associated protein |
| RA | 259,762 | C→A | 5.3% | C66F (TGC→TTC) | ykfH ← | uncharacterized protein |
| RA | 259,937 | T→G | 5.4% | R8R (AGG→CGG) | ykfH ← | uncharacterized protein |
| RA | 295,695 | T→G | 6.0% | E317D (GAA→GAC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 370,428 | T→C | 6.7% | intergenic (+91/‑487) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 370,442 | T→C | 5.4% | intergenic (+105/‑473) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 372,807 | Δ1 bp | 7.8% | intergenic (+40/+184) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 372,808 | G→A | 7.8% | intergenic (+41/+183) | yaiL → / ← frmB | DUF2058 family protein/S‑formylglutathione hydrolase |
| RA | 418,995 | T→G | 18.6% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 476,788 | T→C | 5.7% | V1024V (GTA→GTG) | acrB ← | multidrug efflux system protein |
| RA | 476,794 | A→T | 5.6% | V1022V (GTT→GTA) | acrB ← | multidrug efflux system protein |
| RA | 688,049 | G→T | 5.4% | N262K (AAC→AAA) | ybeZ ← | PhoH‑like heat shock protein |
| RA | 727,989 | C→A | 5.6% | A984E (GCA→GAA) | rhsC → | Rhs family putative polymorphic toxin |
| RA | 733,312 | A→G | 6.6% | pseudogene (1032/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 776,406 | T→A | 5.5% | intergenic (+32/‑118) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 776,421 | T→C | 5.9% | intergenic (+47/‑103) | lysW → / → valZ | tRNA‑Lys/tRNA‑Val |
| RA | 776,600:1 | +T | 7.1% | intergenic (+1/‑3) | valZ → / → lysY | tRNA‑Val/tRNA‑Lys |
| RA | 814,064 | G→T | 5.3% | A13A (GCG→GCT) | moaC → | molybdopterin biosynthesis, protein C |
| RA | 869,909 | G→A | 5.6% | W492* (TGG→TAG) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 959,626 | T→C | 6.9% | intergenic (+58/‑150) | ihfB → / → ycaI | integration host factor (IHF), DNA‑binding protein, beta subunit/ComEC family inner membrane protein |
| RA | 965,308 | G→T | 6.3% | W155L (TGG→TTG) | ycaQ → | DUF1006 family protein with C‑terminal wHTH domain |
| RA | 974,938 | G→A | 5.8% | A1053T (GCA→ACA) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 1,020,168 | A→G | 5.6% | Y81C (TAC→TGC) | helD → | DNA helicase IV |
| RA | 1,079,349 | G→T | 7.2% | C173F (TGT→TTT) | efeB → | deferrrochelatase, periplasmic |
| RA | 1,204,059 | C→T | 6.9% | A173T (GCT→ACT) | tfaE ← | e14 prophage; putative tail fiber assembly protein |
| RA | 1,218,667 | A→G | 13.1% | intergenic (‑48/‑53) | ymgI ← / → ymgJ | uncharacterized protein/uncharacterized protein |
| RA | 1,264,818 | G→T | 7.1% | noncoding (40/67 nt) | rdlA → | sRNA antisense regulator affects LdrA translation; proposed addiction module in LDR‑A repeat, with toxic peptide LdrA |
| RA | 1,282,249 | A→G | 18.2% | intergenic (+267/+273) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,497 | A→G | 5.2% | intergenic (+515/+25) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,282,608 | T→C | 5.6% | noncoding (85/171 nt) T9A (ACT→GCT) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,315,250 | C→T | 6.1% | R131H (CGT→CAT) | trpD ← | fused glutamine amidotransferase (component II) of anthranilate synthase/anthranilate phosphoribosyl transferase |
| RA | 1,404,894 | C→T | 5.5% | A376V (GCG→GTG) | dbpA → | ATP‑dependent RNA helicase, specific for 23S rRNA |
| RA | 1,414,071 | G→A | 7.0% | A143V (GCT→GTT) | racR ← | Rac prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,422,040 | A→G | 8.1% | pseudogene (944/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,060 | G→C | 10.4% | pseudogene (924/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,150 | C→T | 6.8% | pseudogene (834/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,168 | A→C | 6.4% | pseudogene (816/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,422,627 | A→G | 5.8% | pseudogene (357/981 nt) | insH1 ← | IS5 transposase and trans‑activator;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 1,460,567 | A→G | 6.6% | pseudogene (919/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,695 | T→G | 7.4% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,752 | C→T | 9.2% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,460,761 | A→G | 7.9% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,526,201 | C→T | 5.3% | G43G (GGC→GGT) | ydcC → | H repeat‑associated putative transposase |
| RA | 1,536,068 | T→C | 5.4% | T260T (ACA→ACG) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,536,077 | T→C | 5.4% | V257V (GTA→GTG) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,536,083 | A→T | 5.2% | S255S (TCT→TCA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,536,113 | A→G | 5.4% | Y245Y (TAT→TAC) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,546,291 | C→T | 5.9% | intergenic (+43/+364) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,555,977 | C→T | 6.9% | P254P (CCG→CCA) | ddpA ← | D‑ala‑D‑a la transporter subunit |
| RA | 1,561,926 | C→A | 8.7% | E385D (GAG→GAT) | yddW ← | liprotein, glycosyl hydrolase homolog |
| RA | 1,623,580 | A→C | 8.7% | T37P (ACC→CCC) | ydfZ → | selenoprotein, function unknown |
| RA | 1,626,062 | Δ1 bp | 10.0% | pseudogene (481/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,626,063 | Δ1 bp | 10.0% | pseudogene (480/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,626,064 | Δ1 bp | 10.0% | pseudogene (479/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,626,070 | A→T | 10.0% | pseudogene (473/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,629,745 | T→A | 6.9% | A120A (GCA→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,629,762 | T→C | 7.3% | T115A (ACT→GCT) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,629,823 | A→G | 5.7% | G94G (GGT→GGC) | stfQ ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,634,632 | C→A | 7.5% | E71* (GAG→TAG) | essQ ← | Qin prophage; putative S lysis protein |
| RA | 1,703,071 | A→G | 6.4% | A632A (GCA→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,721,425 | C→A | 7.3% | N170K (AAC→AAA) | nemA → | chromate reductase, quinone reductase, FMN‑linked; N‑Ethylmaleimide reductase; old yellow enzyme |
| RA | 1,729,979 | G→A | 7.4% | A115A (GCG→GCA) | sodB → | superoxide dismutase, Fe |
| RA | 1,773,866 | G→T | 5.1% | intergenic (‑308/‑8) | ydiP ← / → ydiQ | putative DNA‑binding transcriptional regulator/putative electron transfer flavoprotein subunit |
| RA | 1,839,472 | G→A | 6.3% | S582S (AGC→AGT) | topB ← | DNA topoisomerase III |
| RA | 1,841,899 | C→A | 6.9% | E123* (GAA→TAA) | selD ← | selenophosphate synthase |
| RA | 1,854,749 | T→G | 5.7% | K281Q (AAA→CAA) | ydjL ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,861,063 | Δ1 bp | 13.0% | intergenic (‑334/‑102) | mipA ← / → yeaG | scaffolding protein for murein synthesizing machinery/protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,861,064 | Δ1 bp | 13.0% | intergenic (‑335/‑101) | mipA ← / → yeaG | scaffolding protein for murein synthesizing machinery/protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,901,618 | G→A | 6.7% | G25G (GGC→GGT) | cspC ← | stress protein, member of the CspA‑family |
| RA | 1,903,085 | Δ1 bp | 8.3% | intergenic (‑62/‑97) | mgrB ← / → yobH | regulatory peptide for PhoPQ, feedback inhibition/uncharacterized protein |
| RA | 1,914,028 | G→A | 5.3% | A754A (GCG→GCA) | yebT → | MCE domain protein |
| RA | 1,948,950 | G→T | 9.3% | P772H (CCC→CAC) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,980,410 | C→A | 10.7% | A2E (GCA→GAA) | ftnB → | ferritin B, putative ferrous iron reservoir |
| RA | 2,005,645 | T→C | 6.9% | pseudogene (188/312 nt) | yedN ← | pseudogene, IpaH/YopM family |
| RA | 2,030,221 | C→A | 9.0% | intergenic (+54/+54) | hchA → / ← yedV | glyoxalase III and Hsp31 molecular chaperone/putative sensory kinase in two‑component regulatory system with YedW |
| RA | 2,234,454 | G→T | 5.8% | L232M (CTG→ATG) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,236,477 | G→T | 6.7% | R219S (CGT→AGT) | folE ← | GTP cyclohydrolase I |
| RA | 2,298,241 | T→C | 6.3% | intergenic (+369/+346) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,331,996 | G→T | 7.3% | R302S (CGC→AGC) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,399,955 | C→A | 93.4% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,429,745 | G→T | 6.3% | A128A (GCC→GCA) | usg ← | putative semialdehyde dehydrogenase |
| RA | 2,464,580 | A→C | 7.5% | pseudogene (287/291 nt) T139T (ACT→ACG) |
tfaS → yfdK ← |
pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related CPS‑53 (KpLE1) prophage; conserved protein |
| RA | 2,469,155 | C→A | 7.4% | L56M (CTG→ATG) | yfdS → | CPS‑53 (KpLE1) prophage; uncharacterized protein |
| RA | 2,639,211 | C→A | 5.0% | D492Y (GAT→TAT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain |
| RA | 2,640,532 | C→A | 6.0% | T51T (ACG→ACT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain |
| RA | 2,677,479 | T→C | 9.3% | intergenic (+64/+134) | yphH → / ← glyA | putative DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| RA | 2,719,426 | T→C | 14.0% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,719,536 | G→T | 16.7% | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA of rrnG operon |
| RA | 2,728,649 | G→A | 6.3% | A241V (GCC→GTC) | rluD ← | 23S rRNA pseudouridine(1911,1915,1917) synthase |
| RA | 2,779,130 | T→C | 5.3% | noncoding (67/76 nt) | ileY ← | tRNA‑Ile |
| RA | 2,811,690 | G→T | 6.5% | intergenic (‑57/+142) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,940,902 | G→A | 5.1% | noncoding (47/77 nt) | metW → | tRNA‑Met |
| RA | 2,981,198:1 | +G | 6.5% | coding (304/633 nt) | yqeH → | putative LuxR family transcriptional regulator |
| RA | 2,981,198:2 | +C | 6.5% | coding (304/633 nt) | yqeH → | putative LuxR family transcriptional regulator |
| RA | 2,981,198:3 | +A | 6.5% | coding (304/633 nt) | yqeH → | putative LuxR family transcriptional regulator |
| RA | 3,027,884:1 | +C | 5.4% | coding (650/1518 nt) | lysS ← | lysine tRNA synthetase, constitutive |
| RA | 3,027,884:2 | +T | 5.4% | coding (650/1518 nt) | lysS ← | lysine tRNA synthetase, constitutive |
| RA | 3,027,884:3 | +T | 5.1% | coding (650/1518 nt) | lysS ← | lysine tRNA synthetase, constitutive |
| RA | 3,048,261 | C→G | 17.6% | P181P (CCG→CCC) | ygfB ← | UPF0149 family protein |
| RA | 3,051,320 | G→T | 8.2% | R150R (CGC→CGA) | serA ← | D‑3‑phosphoglycerate dehydrogenase |
| RA | 3,064,718 | T→G | 11.3% | intergenic (‑115/+100) | fbaA ← / ← pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| RA | 3,065,753 | Δ1 bp | 14.9% | coding (229/1164 nt) | pgk ← | phosphoglycerate kinase |
| RA | 3,085,641 | G→A | 5.8% | T135T (ACG→ACA) | gshB → | glutathione synthetase |
| RA | 3,111,676 | G→T | 7.1% | Q266K (CAG→AAG) | yghJ ← | DUF4092 family putative lipoprotein peptidase |
| RA | 3,242,929 | C→A | 5.1% | R66S (CGT→AGT) | yqjD → | membrane‑anchored ribosome‑binding protein |
| RA | 3,263,071 | C→A | 6.8% | intergenic (+110/+504) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,370,215 | G→T | 11.1% | R189S (CGC→AGC) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,408,725 | C→A | 6.1% | Q112K (CAG→AAG) | acrF → | multidrug efflux system protein |
| RA | 3,416,785 | T→C | 5.4% | noncoding (117/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,890 | T→G | 14.3% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,416,899 | A→G | 13.4% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
| RA | 3,434,282 | C→A | 33.8% | G36V (GGC→GTC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,498,239 | A→C | 8.7% | intergenic (+97/+55) | frlR → / ← yhfS | putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,618,160 | A→G | 6.1% | G141G (GGA→GGG) | yhhI → | putative transposase |
| RA | 3,632,681 | A→C | 6.0% | intergenic (+180/+64) | pitA → / ← uspB | phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B |
| RA | 3,707,817 | G→C | 5.3% | R646R (CGC→CGG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,784,192 | C→T | 5.3% | A172T (GCA→ACA) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,818,282 | C→A | 8.2% | D136E (GAC→GAA) | trmH → | tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent |
| RA | 3,904,998 | A→G | 7.9% | intergenic (‑113/+201) | pstS ← / ← glmS | periplasmic phosphate binding protein, high‑affinity/L‑glutamine:D‑fructose‑6‑phosphate aminotransferase |
| RA | 3,928,136 | C→A | 6.1% | S333S (TCC→TCA) | rbsA → | fused D‑ribose transporter subunits of ABC superfamily: ATP‑binding components |
| RA | 3,935,371 | G→T | 5.6% | noncoding (204/1542 nt) | rrsC → | 16S ribosomal RNA of rrnC operon |
| RA | 4,098,583 | G→A | 6.5% | intergenic (+141/‑179) | pfkA → / → sbp | 6‑phosphofructokinase I/sulfate transporter subunit |
| RA | 4,143,498 | G→A | 6.6% | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,165,285 | G→T | 5.2% | intergenic (‑331/‑31) | coaA ← / → thrU | pantothenate kinase/tRNA‑Thr |
| RA | 4,165,449 | C→T | 26.3% | noncoding (50/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,165,450 | A→C | 26.3% | noncoding (51/85 nt) | tyrU → | tRNA‑Tyr |
| RA | 4,166,006 | C→T | 7.6% | R45R (CGC→CGT) | tufB → | translation elongation factor EF‑Tu 2 |
| RA | 4,177,143 | C→A | 17.0% | D622E (GAC→GAA) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,178,501 | G→T | 20.8% | R1075L (CGT→CTT) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,243,419 | C→A | 5.2% | A159D (GCC→GAC) | ubiA → | p‑hydroxybenzoate octaprenyltransferase |
| RA | 4,250,721 | G→A | 8.5% | T65T (ACG→ACA) | yjbM → | uncharacterized protein |
| RA | 4,342,073 | G→T | 9.2% | V58L (GTG→TTG) | yjdJ → | putative acyl‑CoA transferase |
| RA | 4,445,292 | C→A | 11.1% | L45L (CTG→CTT) | fbp ← | fructose‑1,6‑bisphosphatase I |
| RA | 4,498,944 | G→A | 6.0% | pseudogene (119/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,498,963 | A→G | 5.3% | pseudogene (138/785 nt) | insO → | pseudogene, IS911 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,508,660 | T→G | 6.2% | pseudogene (123/504 nt) | insB1 → | IS1 transposase B;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related |
| RA | 4,576,019 | C→A | 6.0% | pseudogene (614/3567 nt) | hsdR ← | pseudogene, premature stop codon, host restriction; endonuclease R |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2208331 | 2209059 | 729 | 11 [9] | [6] 12 | [mlrA] | [mlrA] |
| * | * | ÷ | CP009273 | 3448732 | 3448865 | 134 | 11 [9] | [5] 17 | [gspA] | [gspA] |
| * | * | ÷ | CP009273 | 3792510 | 3792813 | 304 | 11 [9] | [9] 13 | [waaU]–[waaZ] | [waaU],[waaZ] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | 81 (0.830) | 107 (1.100) | 44/250 | NT | 56.9% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 370378 = | NA (NA) | 21 (0.230) | 10/234 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | 372785 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | = 370385 | 149 (2.120) | 17 (0.270) | 7/164 | NT | 11.3% | intergenic (+48/‑530) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | CP009273 | = 372977 | NA (NA) | noncoding (187/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 370386 = | NA (NA) | 14 (0.210) | 6/176 | NT | 14.5% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372878 = | 90 (1.210) | noncoding (88/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 370386 = | NA (NA) | 7 (0.110) | 5/164 | NT | 15.0% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372978 = | 44 (0.620) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 370580 = | 179 (1.840) | 6 (0.090) | 3/166 | NT | 6.9% | noncoding (195/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372986 = | 44 (0.690) | intergenic (+219/+5) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | CP009273 | 370704 = | 81 (0.830) | 10 (0.120) | 3/212 | NT | 15.1% | noncoding (319/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | CP009273 | 372963 = | 44 (0.540) | noncoding (173/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | CP009273 | 1203246 = | 30 (0.310) | 34 (0.400) | 22/218 | NT | 56.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 27 (0.320) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 31 (0.320) | 30 (0.360) | 18/218 | NT | 52.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 27 (0.320) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||