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 | 10,245 | G→A | 5.1% | L84L (CTG→TTG) | satP ← | succinate‑acetate transporter |
| RA | 164,620 | C→T | 5.7% | intergenic (+86/‑110) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 164,621 | A→G | 5.7% | intergenic (+87/‑109) | hrpB → / → mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| RA | 193,565 | C→T | 5.0% | C15C (TGC→TGT) | dxr → | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase |
| RA | 217,593 | G→T | 5.1% | P395T (CCA→ACA) | proS ← | prolyl‑tRNA synthetase |
| RA | 251,639 | A→G | 5.5% | T248A (ACG→GCG) | dinB → | DNA polymerase IV |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 267,148 | Δ1 bp | 5.1% | intergenic (‑181/+36) | ykfK ← / ← yafZ | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 301,237 | C→T | 5.0% | T217T (ACG→ACA) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 349,828 | G→A | 6.6% | intergenic (+256/‑184) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 508,745 | T→G | 9.5% | intergenic (+186/+130) | ybaQ → / ← copA | putative DNA‑binding transcriptional regulator/copper transporter |
| RA | 511,232 | C→A | 5.4% | E50* (GAA→TAA) | copA ← | copper transporter |
| RA | 632,082 | C→A | 5.6% | intergenic (+83/‑100) | cstA → / → ybdD | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein |
| RA | 823,524 | G→A | 5.4% | Y72Y (TAC→TAT) | clsB ← | cardiolipin synthase 2 |
| RA | 828,135 | C→T | 6.2% | G283R (GGG→AGG) | ybhF ← | putative ABC transporter ATPase |
| RA | 870,063 | T→C | 5.1% | I218T (ATA→ACA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 891,882 | C→G | 5.8% | H233Q (CAC→CAG) | nfsA → | nitroreductase A, NADPH‑dependent, FMN‑dependent |
| RA | 892,441 | G→A | 6.3% | A159T (GCG→ACG) ‡ | rimK → | ribosomal protein S6 modification protein |
| RA | 892,443 | G→C | 6.3% | A159A (GCG→GCC) ‡ | rimK → | ribosomal protein S6 modification protein |
| RA | 892,455 | G→C | 6.2% | V163V (GTG→GTC) | rimK → | ribosomal protein S6 modification protein |
| RA | 892,457 | T→A | 6.6% | I164N (ATT→AAT) | rimK → | ribosomal protein S6 modification protein |
| RA | 892,459 | G→C | 6.6% | D165H (GAC→CAC) | rimK → | ribosomal protein S6 modification protein |
| RA | 1,011,082 | C→A | 5.7% | S373R (AGC→AGA) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,112,767 | C→T | 6.0% | G635G (GGC→GGT) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,141,656 | T→A | 7.3% | E904D (GAA→GAT) | rne ← | endoribonuclease; RNA‑binding protein;RNA degradosome binding protein |
| RA | 1,153,208 | T→C | 7.2% | intergenic (+28/‑92) | fabF → / → pabC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| RA | 1,153,213 | T→A | 6.2% | intergenic (+33/‑87) | fabF → / → pabC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| RA | 1,153,214 | T→A | 6.8% | intergenic (+34/‑86) | fabF → / → pabC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| RA | 1,153,219 | G→A | 6.4% | intergenic (+39/‑81) | fabF → / → pabC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II/4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| RA | 1,176,906 | C→T | 6.6% | H96H (CAC→CAT) | lolD → | outer membrane‑specific lipoprotein transporter subunit |
| RA | 1,224,239 | A→T | 8.0% | intergenic (+332/+40) | ycgI → / ← minE | pseudogene/cell division topological specificity factor |
| RA | 1,224,242 | A→T | 5.8% | intergenic (+335/+37) | ycgI → / ← minE | pseudogene/cell division topological specificity factor |
| RA | 1,287,122 | T→G | 8.2% | noncoding (115/171 nt) R19R (AGG→CGG) |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,123 | G→C | 6.8% | noncoding (114/171 nt) R18R (CGC→CGG) ‡ |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,124 | C→A | 6.8% | noncoding (113/171 nt) R18L (CGC→CTC) ‡ |
rttR ← tpr ← |
rtT sRNA, processed from tyrT transcript protamine‑like protein |
| RA | 1,287,672 | C→T | 100% | intergenic (‑50/+110) | tyrT ← / ← purU | tRNA‑Tyr/formyltetrahydrofolate hydrolase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,331,082 | C→A | 5.3% | A12E (GCA→GAA) | topA → | DNA topoisomerase I, omega subunit |
| MC JC | 1,335,035 | Δ726 bp | 100% | ymiA–yciX | ymiA, yciX | |
| RA | 1,344,033 | A→G | 6.7% | L105P (CTG→CCG) | yciT ← | global regulator of transcription; DeoR family |
| RA | 1,345,632 | T→C | 6.3% | T371A (ACG→GCG) | gmr ← | cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of RNase II stability |
| RA | 1,347,745 | C→T | 5.4% | E390K (GAA→AAA) | rnb ← | ribonuclease II |
| RA | 1,352,369 | C→T | 5.0% | R89H (CGT→CAT) | sapF ← | antimicrobial peptide ABC transporter ATPase |
| RA | 1,416,980 | C→A | 6.6% | G136V (GGC→GTC) | recE ← | Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,568,915 | G→A | 5.7% | intergenic (‑92/+39) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,568,917 | A→T | 5.9% | intergenic (‑94/+37) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,568,919 | T→C | 5.9% | intergenic (‑96/+35) | yddW ← / ← gadC | liprotein, glycosyl hydrolase homolog/glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,693,416 | A→G | 5.2% | L283P (CTG→CCG) | uidB ← | glucuronide transporter |
| RA | 1,720,364 | G→T | 5.8% | intergenic (+21/+26) | slyB → / ← slyA | outer membrane lipoprotein/global transcriptional regulator |
| RA | 1,723,266 | G→A | 5.4% | W382* (TGG→TGA) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,753,390 | C→A | 5.2% | T147T (ACG→ACT) | ydhV ← | putative oxidoreductase subunit |
| RA | 1,782,643 | A→T | 5.3% | N417Y (AAC→TAC) | ydiS → | putative oxidoreductase |
| RA | 1,953,532 | C→T | 5.3% | Q31* (CAG→TAG) | cmoB → | tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent |
| RA | 1,963,803 | G→A | 6.9% | A416A (GCC→GCT) | flhA ← | putative flagellar export pore protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 1,987,442 | Δ1 bp | 8.2% | intergenic (+14/+65) | ftnB → / ← yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein |
| RA | 1,987,450:1 | +A | 8.3% | intergenic (+22/+57) | ftnB → / ← yecJ | ferritin B, putative ferrous iron reservoir/DUF2766 family protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,216,925 | A→G | 5.7% | P161P (CCT→CCC) | yehX ← | putative ABC transporter ATPase |
| RA | 2,317,780 | T→C | 6.1% | K699K (AAA→AAG) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,374,672 | G→A | 5.2% | T111M (ACG→ATG) | menE ← | O‑succinylbenzoate‑CoA ligase |
| RA | 2,560,996 | G→T | 13.9% | intergenic (+98/‑372) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein |
| RA | 2,580,798 | T→G | 5.2% | I388S (ATC→AGC) ‡ | tktB → | transketolase 2, thiamine triphosphate‑binding |
| RA | 2,580,799 | C→A | 5.0% | I388I (ATC→ATA) ‡ | tktB → | transketolase 2, thiamine triphosphate‑binding |
| RA | 2,726,044 | T→G | 9.0% | intergenic (‑298/+25) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,726,046 | A→C | 6.6% | intergenic (‑300/+23) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,745,019 | T→A | 5.7% | K107N (AAA→AAT) ‡ | trmD ← | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| RA | 2,745,020 | T→A | 5.2% | K107I (AAA→ATA) ‡ | trmD ← | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| RA | 3,020,511 | C→G | 5.4% | intergenic (+22/‑29) | ssnA → / → ygfM | putative chlorohydrolase/aminohydrolase/putative oxidoreductase |
| RA | 3,037,430 | A→G | 5.1% | L226P (CTG→CCG) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,045,803 | C→T | 6.9% | Q33Q (CAG→CAA) | ygfF ← | putative NAD(P)‑dependent oxidoreductase |
| RA | 3,114,526 | G→T | 6.3% | intergenic (‑174/+24) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,114,527 | A→C | 6.2% | intergenic (‑175/+23) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,114,533 | T→G | 5.1% | intergenic (‑181/+17) | pppA ← / ← sslE | bifunctional prepilin leader peptidase/ methylase/putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,269,956 | T→C | 8.6% | intergenic (+354/+260) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,969 | A→C | 7.3% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,272,209 | A→G | 6.1% | I181I (ATT→ATC) | garR ← | tartronate semialdehyde reductase |
| 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 | 3,698,203 | G→T | 7.4% | A60S (GCA→TCA) | bcsF → | DUF2636 family cellulose production small membrane protein |
| RA | 3,708,428 | T→A | 5.5% | intergenic (‑723/+188) | dppA ← / ← proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| RA | 3,772,467 | C→T | 6.3% | L63L (CTG→TTG) | mtlA → | mannitol‑specific PTS enzyme: IIA, IIB and IIC components |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,262,250 | G→C | 5.8% | G194G (GGG→GGC) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,262,255 | G→C | 5.8% | S196T (AGC→ACC) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,060 | C→T | 29.3% | 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 | 4,482,758 | G→A | 6.4% | H360H (CAC→CAT) | valS ← | valyl‑tRNA synthetase |
| RA | 4,495,814 | C→T | 5.5% | W132* (TGG→TGA) | ahr ← | broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 4,592,095 | A→T | 5.1% | K147* (AAA→TAA) | tsr → | methyl‑accepting chemotaxis protein I, serine sensor receptor |
| RA | 4,606,354 | G→A | 11.5% | noncoding (48/87 nt) | leuQ ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 131559 | 134211 | 2653 | 36 [34] | [32] 35 | [acnB] | [acnB] |
| * | * | ÷ | NC_000913 | 2066258–2066626 | 2066626 | 1–369 | 36 [34] | [34] 36 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 3423749–3424234 | 3424540–3424238 | 5–792 | 35 [33] | [34] 36 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 34 (0.380) | 53 (0.670) | 48/224 | NT | 58.6% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 45 (0.570) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 33 (0.370) | 38 (0.480) | 34/224 | NT | 50.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 45 (0.570) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 94 (1.070) | 69/248 | 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 | = 2580792 | 69 (0.760) | 4 (0.050) | 4/246 | NT | 5.3% | coding (1157/2004 nt) | tktB | transketolase 2, thiamine triphosphate‑binding |
| ? | NC_000913 | = 2580804 | 76 (0.880) | coding (1169/2004 nt) | tktB | transketolase 2, thiamine triphosphate‑binding | |||||
| * | ? | NC_000913 | 2627637 = | 62 (0.690) | 4 (0.050) | 4/244 | NT | 5.8% | coding (1302/2244 nt) | yfgF | cyclic‑di‑GMP phosphodiesterase, anaerobic |
| ? | NC_000913 | 2627672 = | 70 (0.810) | coding (1267/2244 nt) | yfgF | cyclic‑di‑GMP phosphodiesterase, anaerobic | |||||
| * | ? | NC_000913 | = 2856434 | NA (NA) | 3 (0.040) | 3/236 | NT | NA | noncoding (9/24 nt) | REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | = 2856440 | NA (NA) | noncoding (15/24 nt) | REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP198 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | = 3890165 | 100 (1.110) | 7 (0.080) | 7/236 | NT | 6.7% | intergenic (+20/‑71) | tnaA/tnaB | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity |
| ? | NC_000913 | = 3890174 | 104 (1.250) | intergenic (+29/‑62) | tnaA/tnaB | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent/tryptophan transporter of low affinity | |||||
| * | ? | NC_000913 | 4542682 = | 100 (1.110) | 9 (0.110) | 9/238 | NT | 8.2% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 109 (1.300) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542690 | 108 (1.200) | 18 (0.210) | 16/238 | NT | 14.7% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542986 | 109 (1.300) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||