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 | 124,092 | A→C | 5.8% | intergenic (+18/‑307) | aceF → / → lpd | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2/lipoamide dehydrogenase, E3 component is part of three enzyme complexes |
RA | 234,984 | G→T | 13.7% | I80I (ATC→ATA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 234,994 | G→T | 21.7% | S77* (TCA→TAA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,006 | G→T | 11.2% | T73K (ACG→AAG) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,010 | G→T | 21.9% | L72I (CTT→ATT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,019 | C→A | 18.1% | V69L (GTA→TTA) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 235,022 | G→T | 18.8% | H68N (CAT→AAT) | ykfM ← | lethality reduction protein, putative inner membrane protein |
RA | 345,353 | A→G | 7.8% | intergenic (+70/‑370) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
RA | 345,384 | G→C | 5.4% | intergenic (+101/‑339) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
RA | 345,387 | G→A | 5.1% | intergenic (+104/‑336) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
RA | 345,428 | T→C | 7.9% | intergenic (+145/‑295) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
RA | 353,486 | A→T | 8.8% | intergenic (+321/+16) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
RA | 353,489 | C→T | 8.2% | intergenic (+324/+13) | codA → / ← cynR | cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor |
RA | 360,157 | T→G | 8.6% | intergenic (‑91/+504) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,173 | C→A | 7.0% | intergenic (‑107/+488) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,197 | T→A | 6.4% | intergenic (‑131/+464) | lacZ ← / ← lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
RA | 360,752 | A→G | 100% | V331A (GTG→GCG) | lacI ← | DNA‑binding transcriptional repressor |
JC | 361,139 | +GCCA | 9.3% | coding (605/1083 nt) | lacI ← | DNA‑binding transcriptional repressor |
RA | 361,806 | G→A | 100% | intergenic (‑63/+14) | lacI ← / ← mhpR | DNA‑binding transcriptional repressor/mhp operon transcriptional activator |
RA | 370,703 | A→G | 5.1% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
RA | 450,333 | A→T | 8.6% | intergenic (+88/‑256) | bolA → / → tig | stationary‑phase morphogene, transcriptional repressor for mreB; also regulator for dacA, dacC, and ampC/peptidyl‑prolyl cis/trans isomerase (trigger factor) |
RA | 776,694 | T→A | 5.6% | intergenic (+16/‑131) | lysY → / → lysZ | tRNA‑Lys/tRNA‑Lys |
RA | 877,776 | A→C | 5.5% | F139V (TTT→GTT) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
RA | 1,118,506 | A→T | 11.5% | L75Q (CTA→CAA) | yceB ← | lipoprotein, DUF1439 family |
RA | 1,282,421 | A→T | 14.3% | intergenic (+439/+101) | narI → / ← rttR | nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript |
JC JC | 1,376,043 | IS5 (–) +4 bp | 100% | pseudogene (10‑13/126 nt) | ycjV → | pseudogene; putative ATP‑binding component of a transport system |
JC JC | 1,427,903 | IS3 (–) +3 bp | 21.6% | coding (27‑29/591 nt) | pinR ← | Rac prophage; putative site‑specific recombinase |
RA | 1,460,752 | C→T | 6.6% | pseudogene (1104/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
RA | 1,628,207 | G→A | 95.0% | G110E (GGA→GAA) | pinQ → | Qin prophage; putative site‑specific recombinase |
RA | 1,702,966 | T→A | 8.0% | R597R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 1,703,062 | T→A | 10.6% | R629R (CGT→CGA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 1,703,071 | A→T | 8.3% | A632A (GCA→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 1,703,101 | C→G | 9.7% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
RA | 2,170,708 | G→T | 9.6% | intergenic (‑25/+283) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,713 | C→A | 28.9% | intergenic (‑30/+278) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,724 | G→T | 31.2% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,757 | T→A | 14.6% | intergenic (‑74/+234) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,170,758 | C→A | 13.5% | intergenic (‑75/+233) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
RA | 2,178,937 | A→T | 10.2% | intergenic (‑157/+66) | thiM ← / ← rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
RA | 2,298,128 | C→T | 6.4% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
RA | 2,298,492 | A→G | 5.0% | intergenic (+620/+95) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
RA | 2,303,607 | A→C | 6.9% | L93R (CTG→CGG) | ada ← | fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase |
RA | 2,463,906 | C→A | 19.9% | Q433K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,463,910 | G→T | 17.4% | R434I (AGA→ATA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,463,915 | C→A | 12.8% | Q436K (CAA→AAA) | gtrS → | serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage |
RA | 2,711,673 | A→C | 9.2% | V72G (GTT→GGT) | yfiF ← | putative methyltransferase |
JC | 2,713,645 | +CCTGCGC | 11.7% | coding (334/2661 nt) | pka → | protein lysine acetyltransferase |
RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
RA | 2,785,712 | C→A | 29.3% | H361N (CAC→AAC) | gabD → | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
RA | 2,811,504 | T→C | 5.4% | intergenic (‑10/+53) | argZ ← / ← argY | tRNA‑Arg/tRNA‑Arg |
JC | 2,811,717 | Δ134 bp | 5.5% | [argV] | [argV] | |
RA | 2,834,252 | A→T | 7.8% | E457V (GAG→GTG) | ascF → | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
RA | 2,834,267 | A→T | 5.8% | E462V (GAG→GTG) | ascF → | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
RA | 2,835,291 | T→G | 13.1% | C315G (TGC→GGC) | ascB → | cryptic 6‑phospho‑beta‑glucosidase |
RA | 3,263,315 | T→C | 6.0% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
RA | 3,263,460 | C→A | 12.5% | intergenic (+499/+115) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
RA | 3,263,502 | C→T | 8.4% | intergenic (+541/+73) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
RA | 3,385,479 | C→G | 10.4% | intergenic (‑92/+338) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,385,487 | A→T | 7.5% | intergenic (‑100/+330) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,385,516 | A→T | 11.8% | intergenic (‑129/+301) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,385,518 | G→C | 10.4% | intergenic (‑131/+299) | tldD ← / ← yhdP | putative peptidase/DUF3971‑AsmA2 domains protein |
RA | 3,416,890 | T→G | 9.1% | noncoding (12/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
RA | 3,416,899 | A→G | 5.7% | noncoding (3/120 nt) | rrfF ← | 5S ribosomal RNA of rrnD operon |
RA | 3,449,090 | C→A | 5.5% | P52T (CCA→ACA) | gspC → | general secretory pathway component, cryptic |
RA | 3,469,859 | G→T | 9.6% | intergenic (‑60/+107) | yheO ← / ← fkpA | putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
RA | 3,519,657 | G→T | 100% | intergenic (‑149/‑171) | nudE ← / → yrfF | adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein |
RA | 3,546,339 | C→A | 11.2% | intergenic (‑507/‑105) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
RA | 3,547,642 | T→A | 12.9% | L400Q (CTG→CAG) | malT → | mal regulon transcriptional activator |
RA | 3,721,485 | T→G | 10.7% | Y416S (TAC→TCC) | xylB ← | xylulokinase |
RA | 3,786,687 | C→A | 5.8% | L119F (TTG→TTT) | yibB ← | YibB family protein, function unknown |
RA | 3,816,601 | A→T | 94.3% | H281L (CAC→CTC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
RA | 3,822,339 | A→C | 9.9% | Q12P (CAA→CCA) ‡ | xanP → | xanthine permease |
RA | 3,822,340 | A→C | 14.5% | Q12H (CAA→CAC) ‡ | xanP → | xanthine permease |
RA | 3,871,017 | A→T | 6.7% | intergenic (‑192/+48) | yidB ← / ← gyrB | DUF937 family protein/DNA gyrase, subunit B |
RA | 3,960,036 | G→A | 91.5% | R87H (CGC→CAC) | rho → | transcription termination factor |
RA | 4,143,375 | A→G | 6.6% | intergenic (‑349/+249) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
RA | 4,143,544 | C→T | 6.6% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
RA | 4,297,846 | C→A | 86.4% | M150I (ATG→ATT) | alsE ← | allulose‑6‑phosphate 3‑epimerase |
RA | 4,315,765 | A→G | 5.5% | intergenic (‑207/+451) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
RA | 4,361,085 | A→C | 9.3% | N82H (AAC→CAC) | groL → | Cpn60 chaperonin GroEL, large subunit of GroESL |
RA | 4,411,145 | T→G | 10.5% | L450R (CTG→CGG) | ulaA → | L‑ascorbate‑specific enzyme IIC permease component of PTS |
RA | 4,557,158 | T→C | 5.3% | G393G (GGA→GGG) | mdtM ← | multidrug efflux system protein |
RA | 4,604,240 | T→A | 6.3% | intergenic (+163/+257) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
RA | 4,604,261 | A→G | 7.9% | intergenic (+184/+236) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | CP009273 | 373843 | 375099 | 1257 | 140 [137] | [137] 141 | frmA–[frmR] | frmA,[frmR] |
* | * | ÷ | CP009273 | 4100623 | 4101505 | 883 | 141 [135] | [138] 141 | tpiA | tpiA |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | CP009273 | 360104 = | 133 (0.600) | 124 (0.560) | 69/276 | NT | 48.2% | 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 | = 360278 | NA (NA) | 21752 (104.610) +TTAATTAA |
196/260 | NT | 99.0% | intergenic (‑212/+383) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 361823 | 224 (1.010) | coding (831/834 nt) | mhpR | mhp operon transcriptional activator | |||||
* | ? | CP009273 | 360652 = | 204 (0.920) | 20871 (142.290) +46 bp |
183/184 | NT | 99.4% | intergenic (‑586/+9) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
? | CP009273 | = 1317577 | 193 (0.870) | coding (101/882 nt) | yciV | PHP domain protein | |||||
* | ? | CP009273 | = 361823 | 224 (1.010) | 11 (0.050) +TTAATTAA |
6/260 | NT | 5.3% | coding (831/834 nt) | mhpR | mhp operon transcriptional activator |
? | CP009273 | 4033991 = | 194 (0.880) | noncoding (115/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
* | ? | CP009273 | 376716 = | NA (NA) | 189 (0.860) | 110/276 | NT | 85.5% | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA |
? | CP009273 | 566411 = | 32 (0.140) | coding (63/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
* | ? | CP009273 | = 378046 | NA (NA) | 222 (1.010) | 118/276 | NT | 87.4% | intergenic (+11/+1) | insD1/yaiX | IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase |
? | CP009273 | = 566415 | 32 (0.140) | coding (67/552 nt) | ybcL | inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family | |||||
* | ? | CP009273 | 776825 = | 139 (0.630) | 20 (0.090) +G |
7/274 | NT | 12.3% | noncoding (1/76 nt) | lysZ | tRNA‑Lys |
? | CP009273 | = 2514488 | 147 (0.670) | noncoding (216/1345 nt) | IS186 | repeat region | |||||
* | ? | CP009273 | 1203246 = | 6 (0.030) | 164 (0.840) | 94/244 | NT | 93.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | 1205075 = | 19 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 1203261 | 6 (0.030) | 195 (1.000) | 107/244 | NT | 94.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | CP009273 | = 1205058 | 19 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | CP009273 | = 3385461 | 221 (1.000) | 14 (0.080) | 13/210 | NT | 8.4% | noncoding (27/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences |
? | CP009273 | 3385736 = | 138 (0.820) | noncoding (302/308 nt) | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | REP245 (repetitive extragenic palindromic) element; contains 7 REP sequences | |||||
* | ? | CP009273 | 4532499 = | 173 (0.780) | 22 (0.110) | 15/258 | NT | 10.8% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
? | CP009273 | 4532813 = | 201 (0.970) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
* | ? | CP009273 | = 4532507 | 178 (0.810) | 22 (0.110) | 13/258 | NT | 10.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
? | CP009273 | = 4532803 | 201 (0.970) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |