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 | 855 | T→G | 5.1% | R173R (CGT→CGG) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 864 | A→T | 5.3% | A176A (GCA→GCT) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 865 | A→T | 5.3% | S177C (AGC→TGC) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 872 | T→A | 6.0% | I179N (ATT→AAT) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 874 | C→A | 6.4% | P180T (CCG→ACG) | thrA → | Bifunctional aspartokinase/homoserine dehydrogenase 1 |
| RA | 43,677 | G→A | 5.0% | E164K (GAA→AAA) | fixB → | putative electron transfer flavoprotein, NAD/FAD‑binding domain and ETFP adenine nucleotide‑binding domain‑like protein |
| RA | 89,152 | A→T | 5.1% | intergenic (+120/‑482) | cra → / → mraZ | transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor |
| RA | 139,246 | A→G | 5.6% | F660F (TTT→TTC) | gcd ← | glucose dehydrogenase |
| RA | 164,558 | T→A | 5.4% | intergenic (+24/‑172) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 194,272 | A→G | 5.8% | H251R (CAC→CGC) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 285,197 | A→G | 6.9% | intergenic (+29/‑198) | yagF → / → yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| RA | 285,199 | T→A | 7.0% | intergenic (+31/‑196) | yagF → / → yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| RA | 285,202 | T→A | 7.9% | intergenic (+34/‑193) | yagF → / → yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| RA | 285,204 | C→T | 7.0% | intergenic (+36/‑191) | yagF → / → yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| RA | 334,215 | G→T | 5.1% | T73T (ACC→ACA) | yahB ← | putative DNA‑bindng transcriptional regulator |
| RA | 337,740 | G→A | 6.0% | L321L (CTG→CTA) | yahF → | putative NAD(P)‑binding succinyl‑CoA synthase |
| RA | 366,833 | A→T | 6.0% | F226L (TTT→TTA) | lacI ← | lactose‑inducible lac operon transcriptional repressor |
| RA | 414,832 | G→T | 5.4% | H308N (CAT→AAT) | sbcC ← | exonuclease, dsDNA, ATP‑dependent |
| RA | 475,971 | C→G | 7.7% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 6.6% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 517,383 | A→T | 6.9% | intergenic (+21/+42) | fetB → / ← ybbN | iron export ABC transporter permease; peroxide resistance protein/DnaK co‑chaperone, thioredoxin‑like protein |
| JC JC | 523,077 | IS2 (+) +5 bp | 25.9% | intergenic (+247/‑180) | ybbP → / → rhsD | putative ABC transporter permease/Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 525,924 | C→T | 6.8% | Y888Y (TAC→TAT) | rhsD → | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 544,323 | C→G | 5.1% | D324H (GAC→CAC) | allC ← | allantoate amidohydrolase |
| RA | 578,331 | G→T | 7.8% | A75A (GCG→GCT) R2L (CGA→CTA) |
rzpD → rzoD → |
DLP12 prophage; putative murein endopeptidase DLP12 prophage; putative lipoprotein |
| RA | 578,809 | T→C | 5.4% | T29A (ACA→GCA) | borD ← | DLP12 prophage; putative lipoprotein |
| RA | 580,020 | G→A | 5.5% | R47R (AGG→AGA) | ybcW → | DLP12 prophage; uncharacterized protein |
| RA | 580,115 | C→T | 7.5% | intergenic (+29/+136) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 580,119 | A→G | 7.3% | intergenic (+33/+132) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 580,120 | C→T | 7.2% | intergenic (+34/+131) | ybcW → / ← ylcI | DLP12 prophage; uncharacterized protein/DUF3950 family protein, DLP12 prophage |
| RA | 581,042 | T→G | 9.5% | L70R (CTG→CGG) | nohD → | DLP12 prophage; DNA packaging protein |
| RA | 696,410 | C→T | 6.5% | intergenic (+134/+20) | ubiF → / ← glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln |
| RA | 696,411 | G→T | 6.6% | intergenic (+135/+19) | ubiF → / ← glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln |
| RA | 696,412 | A→C | 7.5% | intergenic (+136/+18) | ubiF → / ← glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln |
| RA | 696,413 | A→G | 6.7% | intergenic (+137/+17) | ubiF → / ← glnX | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase/tRNA‑Gln |
| RA | 733,154 | T→C | 5.6% | L1191P (CTG→CCG) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 755,646 | C→A | 7.6% | Y29* (TAC→TAA) | sdhD → | succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 756,054 | C→T | 42.8% | Q50* (CAA→TAA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| JC | 756,291 | Δ11 bp | 18.8% | coding (385‑395/1767 nt) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 756,423 | C→T | 24.3% | Q173* (CAG→TAG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 757,857 | G→T | 9.1% | E57* (GAA→TAA) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 816,956 | C→A | 5.4% | intergenic (‑309/‑88) | ybhK ← / → moaA | putative CofD superfamily transferase/molybdopterin biosynthesis protein A |
| RA | 854,868 | C→T | 5.1% | E293K (GAA→AAA) | ldtB ← | L,D‑transpeptidase linking Lpp to murein |
| RA | 944,073 | C→T | 5.9% | T14M (ACG→ATG) | dmsC → | dimethyl sulfoxide reductase, anaerobic, subunit C |
| RA | 1,046,842 | C→A | 5.1% | T368T (ACG→ACT) | gfcD ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,071,029 | G→A | 5.9% | T246M (ACG→ATG) | rutD ← | putative reactive intermediate detoxifying aminoacrylate hydrolase |
| RA | 1,071,673 | C→T | 6.2% | P31P (CCG→CCA) | rutD ← | putative reactive intermediate detoxifying aminoacrylate hydrolase |
| RA | 1,097,348 | A→G | 7.8% | intergenic (+519/+217) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,149,544 | Δ1 bp | 5.4% | coding (786/954 nt) | fabH → | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III |
| RA | 1,287,024 | G→A | 5.3% | intergenic (+498/+42) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,287,047 | C→T | 5.7% | intergenic (+521/+19) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
| RA | 1,355,187 | A→G | 5.5% | V95A (GTG→GCG) ‡ | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,355,188 | C→T | 5.5% | V95M (GTG→ATG) ‡ | sapB ← | antimicrobial peptide transport ABC transporter permease |
| RA | 1,375,962 | C→G | 5.1% | Q334E (CAG→GAG) | ycjQ → | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,429,021 | T→A | 7.2% | intergenic (+37/‑28) | lomR → / → stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| RA | 1,429,022 | T→A | 7.1% | intergenic (+38/‑27) | lomR → / → stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| RA | 1,429,024 | A→C | 7.1% | intergenic (+40/‑25) | lomR → / → stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| RA | 1,429,027 | C→T | 7.4% | intergenic (+43/‑22) | lomR → / → stfR | pseudogene, Rac prophage lom homolog;Phage or Prophage Related; interrupted by IS5 and N‑ter deletion/Rac prophage; putative tail fiber protein |
| RA | 1,429,069 | T→A | 10.7% | G7G (GGT→GGA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,072 | A→C | 10.1% | V8V (GTA→GTC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,111 | A→C | 12.3% | T21T (ACA→ACC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,114 | C→T | 12.6% | I22I (ATC→ATT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,126 | A→C | 11.2% | A26A (GCA→GCC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,128 | A→G | 11.4% | K27R (AAA→AGA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,160 | C→G | 8.7% | L38V (CTG→GTG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,164 | C→G | 8.5% | A39G (GCC→GGC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,171 | A→G | 7.5% | E41E (GAA→GAG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,204 | C→T | 7.7% | D52D (GAC→GAT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,816 | C→T | 6.7% | S256S (AGC→AGT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,820 | A→G | 6.8% | S258G (AGT→GGT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,823 | A→C | 6.8% | S259R (AGT→CGT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,851 | G→A | 6.1% | G268E (GGA→GAA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,858 | C→T | 6.5% | S270S (TCC→TCT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,861 | G→C | 6.3% | A271A (GCG→GCC) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,863 | A→G | 6.3% | K272R (AAG→AGG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,888 | C→T | 5.5% | N280N (AAC→AAT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,897 | T→A | 5.3% | S283S (TCT→TCA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,906 | G→A | 5.9% | T286T (ACG→ACA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,429,914 | G→A | 5.9% | G289E (GGA→GAA) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,567,466 | G→C | 6.0% | intergenic (‑326/+38) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,567,467 | G→T | 5.5% | intergenic (‑327/+37) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,567,469 | A→T | 6.0% | intergenic (‑329/+35) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,567,471 | A→C | 7.7% | intergenic (‑331/+33) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,567,472 | G→C | 5.6% | intergenic (‑332/+32) | dosC ← / ← yddW | diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator/liprotein, glycosyl hydrolase homolog |
| RA | 1,585,149 | Δ1 bp | 5.3% | coding (1338/2280 nt) | ydeP ← | putative oxidoreductase |
| RA | 1,592,875 | C→T | 5.3% | pseudogene (1251/1461 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,603,934 | C→T | 7.0% | R306C (CGC→TGC) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,612,094 | T→A | 6.2% | T78S (ACC→TCC) | yneG ← | DUF4186 family protein |
| RA | 1,636,690 | C→T | 5.5% | intergenic (‑323/‑66) | nohQ ← / → ynfO | pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage |
| RA | 1,655,299 | G→A | 5.9% | intergenic (‑158/+48) | rspA ← / ← ynfA | bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein |
| RA | 1,662,350 | C→T | 100% | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,663,395 | G→A | 6.0% | G136R (GGG→AGG) | ynfG → | oxidoreductase, Fe‑S subunit |
| RA | 1,674,955 | A→T | 5.7% | intergenic (+8/+17) | tqsA → / ← pntB | pheromone AI‑2 transporter/pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,678,903 | T→C | 5.4% | D159D (GAT→GAC) | ydgH → | DUF1471 family periplasmic protein |
| RA | 1,721,397 | T→A | 5.6% | V45D (GTT→GAT) | ydhJ → | putative membrane fusion protein (MFP) of YdhJK efflux pump |
| RA | 1,867,030 | G→A | 5.2% | R41R (CGG→CGA) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
| RA | 1,925,473 | G→C | 5.3% | E12Q (GAG→CAG) | yobB → | C‑N hydrolase family protein |
| RA | 1,932,094 | C→G | 7.6% | intergenic (+35/+21) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,095 | T→A | 7.4% | intergenic (+36/+20) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| RA | 1,932,096 | C→G | 7.3% | intergenic (+37/+19) | purT → / ← eda | phosphoribosylglycinamide formyltransferase 2/KHG/KDPG aldolase; 2‑dehydro‑3‑deoxy‑phosphogluconate/4‑hydroxy‑2‑ oxoglutarate aldolase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| 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 | 2,216,776 | C→T | 5.2% | G211D (GGT→GAT) | yehX ← | putative ABC transporter ATPase |
| RA | 2,304,649 | C→T | 21.4% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,085 | A→G | 6.5% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 6.2% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 6.4% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,357,653 | A→G | 7.0% | L250L (CTA→CTG) | yfaD → | transposase_31 family protein |
| RA | 2,412,639 | T→A | 5.3% | intergenic (‑45/+38) | yfbU ← / ← yfbV | UPF0304 family protein/UPF0208 family inner membrane protein |
| RA | 2,412,640 | G→T | 5.3% | intergenic (‑46/+37) | yfbU ← / ← yfbV | UPF0304 family protein/UPF0208 family inner membrane protein |
| RA | 2,412,642 | G→C | 5.1% | intergenic (‑48/+35) | yfbU ← / ← yfbV | UPF0304 family protein/UPF0208 family inner membrane protein |
| RA | 2,432,985 | A→G | 6.7% | intergenic (‑43/+27) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,990 | G→C | 6.3% | intergenic (‑48/+22) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,432,995 | C→T | 5.9% | intergenic (‑53/+17) | folC ← / ← accD | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase/acetyl‑CoA carboxylase, beta (carboxyltransferase) subunit |
| RA | 2,440,295 | A→T | 6.6% | intergenic (‑175/+90) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,296 | T→G | 6.7% | intergenic (‑176/+89) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,297 | C→A | 6.8% | intergenic (‑177/+88) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,440,298 | A→T | 6.7% | intergenic (‑178/+87) | yfcJ ← / ← fabB | putative arabinose efflux transporter/3‑oxoacyl‑[acyl‑carrier‑protein] synthase I |
| RA | 2,462,677 | A→T | 5.8% | intergenic (+31/‑335) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,678 | T→A | 5.6% | intergenic (+32/‑334) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,462,679 | A→T | 5.6% | intergenic (+33/‑333) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,533,418 | T→A | 5.3% | intergenic (+38/‑346) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,560,996 | G→T | 16.2% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,607,935 | C→A | 6.5% | A340E (GCG→GAG) | hyfF → | hydrogenase 4, membrane subunit |
| RA | 2,642,793 | G→T | 5.4% | R18S (CGC→AGC) | rodZ ← | MreB assembly cytoskeletal protein |
| RA | 2,666,510 | T→A | 5.1% | L359* (TTA→TAA) | csiE → | stationary phase inducible protein |
| RA | 2,684,983 | A→T | 5.5% | S175S (TCT→TCA) | glyA ← | serine hydroxymethyltransferase |
| RA | 2,691,169 | A→T | 6.1% | noncoding (172/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,171 | T→A | 5.9% | noncoding (170/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,691,173 | A→T | 5.9% | noncoding (168/184 nt) | glmY ← | sRNA activator of glmS mRNA, glmZ processing antagonist |
| RA | 2,704,304 | A→G | 5.6% | intergenic (‑241/+31) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,306 | A→T | 5.7% | intergenic (‑243/+29) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,704,308 | C→T | 5.8% | intergenic (‑245/+27) | rnc ← / ← lepB | RNase III/leader peptidase (signal peptidase I) |
| RA | 2,771,583 | C→T | 5.4% | L146L (CTG→TTG) | yfjT → | CP4‑57 prophage; putative periplasmic protein |
| RA | 2,947,465 | Δ1 bp | 16.7% | intergenic (+2/‑32) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,947,467 | A→C | 16.7% | intergenic (+4/‑30) | metZ → / → metW | tRNA‑Met/tRNA‑Met |
| RA | 2,981,039 | T→C | 5.0% | I382V (ATC→GTC) | araE ← | arabinose transporter |
| RA | 3,031,616 | G→A | 5.6% | G84S (GGT→AGT) | uacT → | uric acid permease |
| RA | 3,125,574 | A→C | 5.9% | F317V (TTT→GTT) | glcE ← | glycolate oxidase FAD binding subunit |
| RA | 3,157,277 | C→A | 5.3% | R219S (CGC→AGC) | dkgA → | 2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,165,154 | T→A | 5.8% | M274L (ATG→TTG) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,165,155 | T→A | 5.8% | Q273H (CAA→CAT) | parC ← | DNA topoisomerase IV, subunit A |
| RA | 3,239,609 | T→G | 6.2% | intergenic (+64/‑335) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,610 | C→G | 6.7% | intergenic (+65/‑334) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,239,611 | C→A | 6.5% | intergenic (+66/‑333) | alx → / → sstT | putative membrane‑bound redox modulator/sodium:serine/threonine symporter |
| RA | 3,253,616 | A→G | 5.0% | I200T (ATT→ACT) | yhaJ ← | LysR family putative transcriptional regulator |
| RA | 3,439,588 | G→C | 5.8% | intergenic (‑79/+28) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,439,589 | G→C | 6.0% | intergenic (‑80/+27) | yhdN ← / ← rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| RA | 3,530,672 | G→C | 8.0% | intergenic (+20/+43) | hslO → / ← yhgE | heat shock protein Hsp33/DUF4153 family putative inner membrane protein |
| RA | 3,533,559 | G→A | 6.3% | G248S (GGC→AGC) | pck → | phosphoenolpyruvate carboxykinase [ATP] |
| 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 | 3,690,623 | G→A | 5.7% | A662V (GCG→GTG) | bcsB ← | regulator of cellulose synthase, cyclic di‑GMP binding |
| RA | 3,809,681 | T→A | 6.8% | V381D (GTT→GAT) ‡ | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| RA | 3,809,682 | T→A | 6.8% | V381V (GTT→GTA) ‡ | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| RA | 3,809,683 | T→A | 6.8% | S382T (TCC→ACC) | waaA → | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| JC | 3,815,859 | Δ82 bp | 48.8% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,819,816 | A→C | 5.2% | L452R (CTT→CGT) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 4,175,146 | Δ1 bp | 100% | intergenic (‑120/‑242) | coaA ← / → thrU | pantothenate kinase/tRNA‑Thr |
| RA | 4,296,060 | C→T | 42.1% | intergenic (+266/+376) | 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 | 4,312,080 | G→C | 5.3% | intergenic (‑38/+21) | alsB ← / ← alsR | D‑allose ABC transporter periplasmic binding protein/d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR |
| RA | 4,356,445 | A→T | 6.7% | intergenic (‑34/+25) | dtpC ← / ← cadA | dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible |
| RA | 4,356,446 | A→T | 6.7% | intergenic (‑35/+24) | dtpC ← / ← cadA | dipeptide and tripeptide permease/lysine decarboxylase, acid‑inducible |
| RA | 4,599,416 | A→G | 5.2% | L9P (CTT→CCT) | opgB ← | OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 131572 | 134236 | 2665 | 37 [35] | [35] 37 | acnB | acnB |
| * | * | ÷ | NC_000913 | 3423760–3424234 | 3424591–3424238 | 5–832 | 37 [36] | [36] 39 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 73382 | 52 (0.590) | 5 (0.060) | 5/244 | NT | 8.9% | coding (1140/1611 nt) | thiP | thiamine/thiamine pyrophosphate ABC transporter permease |
| ? | NC_000913 | = 73393 | 53 (0.640) | coding (1129/1611 nt) | thiP | thiamine/thiamine pyrophosphate ABC transporter permease | |||||
| * | ? | NC_000913 | 79973 = | 65 (0.740) | 4 (0.050) | 4/242 | NT | 6.8% | coding (892/1401 nt) | leuC | 3‑isopropylmalate dehydratase large subunit |
| ? | NC_000913 | 80003 = | 48 (0.580) | coding (862/1401 nt) | leuC | 3‑isopropylmalate dehydratase large subunit | |||||
| * | ? | NC_000913 | 244129 = | NA (NA) | 5 (0.060) | 5/246 | NT | 6.5% | noncoding (1/135 nt) | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913 | 244213 = | 72 (0.860) | noncoding (85/135 nt) | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP17 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | = 315838 | NA (NA) | 3 (0.030) | 3/254 | NT | NA | noncoding (610/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 315862 | NA (NA) | noncoding (634/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1155242 = | 60 (0.680) | 7 (0.080) | 7/256 | NT | 9.6% | coding (119/642 nt) | tmk | thymidylate kinase |
| ? | NC_000913 | = 1560603 | 73 (0.840) | coding (327/1023 nt) | ddpB | D,D‑dipeptide ABC transporter permease | |||||
| * | ? | NC_000913 | 1170033 = | 80 (0.910) | 5 (0.060) | 5/256 | NT | 6.1% | coding (342/963 nt) | ldtC | L,D‑transpeptidase linking Lpp to murein |
| ? | NC_000913 | = 1340069 | 75 (0.860) | coding (740/765 nt) | pgpB | phosphatidylglycerophosphatase B | |||||
| * | ? | NC_000913 | 1207790 = | 38 (0.430) | 47 (0.610) | 41/226 | NT | 55.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 41 (0.530) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 38 (0.430) | 39 (0.510) | 37/226 | NT | 51.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 41 (0.530) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 122 (1.440) | 92/250 | 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 | 1570598 = | 111 (1.270) | 7 (0.090) +CCGTTACCGTTAAAC |
7/228 | NT | 6.7% | intergenic (‑109/+47) | gadC/gadB | glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent |
| ? | NC_000913 | 3666176 = | 111 (1.270) | intergenic (‑366/+4) | gadX/gadA | acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent | |||||
| * | ? | NC_000913 | 1592628 = | NA (NA) | 4 (0.050) | 4/236 | NT | NA | intergenic (‑186/+37) | hipB/yneO | antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog |
| ? | NC_000913 | 1592659 = | NA (NA) | intergenic (‑217/+6) | hipB/yneO | antitoxin of HipAB toxin‑antitoxin system/pseudogene, AidA homolog | |||||
| * | ? | NC_000913 | 2729475 = | 50 (0.570) | 5 (0.060) | 4/238 | NT | 10.4% | intergenic (‑31/+141) | gltW/rrsG | tRNA‑Glu/16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 4168363 | 40 (0.490) | intergenic (+163/‑9) | rrsB/gltT | 16S ribosomal RNA of rrnB operon/tRNA‑Glu | |||||
| * | ? | NC_000913 | = 3411413 | 95 (1.080) | 11 (0.140) | 10/236 | NT | 11.6% | coding (143/297 nt) | fis | global DNA‑binding transcriptional dual regulator |
| ? | NC_000913 | 3411671 = | 81 (1.010) | coding (19/885 nt) | yhdJ | DNA adenine methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 4188500 | 64 (0.730) | 4 (0.050) | 4/244 | NT | 5.9% | coding (3151/4224 nt) | rpoC | RNA polymerase, beta prime subunit |
| ? | NC_000913 | = 4188510 | 66 (0.800) | coding (3161/4224 nt) | rpoC | RNA polymerase, beta prime subunit | |||||
| * | ? | NC_000913 | 4542682 = | 79 (0.900) | 40 (0.490) | 36/240 | NT | 34.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 82 (1.010) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 78 (0.890) | 53 (0.650) | 46/240 | NT | 40.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 82 (1.010) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||