mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 40,450 | A→G | 8.9% | F494F (TTT→TTC) | caiT ← | putative transporter |
| RA | 234,230 | T→C | 9.7% | I185V (ATA→GTA) | gloB ← | hydroxyacylglutathione hydrolase |
| RA | 254,876 | T→A | 4.4% | N281Y (AAT→TAT) | pepD ← | aminoacyl‑histidine dipeptidase (peptidase D) |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,168 | G→T | 4.6% | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 738,600 | A→C | 5.2% | K170T (AAA→ACA) | ybfD → | H repeat‑associated putative transposase |
| RA | 738,604 | C→T | 5.3% | T171T (ACC→ACT) | ybfD → | H repeat‑associated putative transposase |
| RA | 828,729 | T→C | 6.0% | M85V (ATG→GTG) | ybhF ← | putative ABC transporter ATPase |
| RA | 1,111,908 | C→A | 9.8% | S349* (TCG→TAG) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase, nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,217,099 | T→C | 7.3% | intergenic (+103/‑229) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,395,146 | A→G | 6.7% | R259R (CGT→CGC) | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,482,252 | C→T | 7.7% | intergenic (+51/+3) | ynbD → / ← azoR | putative phosphatase inner membrane protein/NADH‑azoreductase, FMN‑dependent |
| RA | 1,904,420 | A→T | 6.6% | I176F (ATC→TTC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,953,932 | T→C | 3.7% | V164A (GTG→GCG) | cmoB → | tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent |
| JC | 1,970,869 | Δ3 bp | 4.7% | coding (114‑116/1602 nt) | tap ← | methyl‑accepting protein IV |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,290,728 | T→A | 6.4% | D77E (GAT→GAA) | narP → | response regulator in two‑component regulatory system with NarQ |
| RA | 2,507,626 | G→T | 6.9% | D89E (GAC→GAA) | fryC ← | putative enzyme IIC component of PTS |
| RA | 2,708,131 | G→T | 5.8% | P208T (CCG→ACG) | rseB ← | anti‑sigma E factor, binds RseA |
| RA | 2,769,201 | A→G | 4.5% | Q180R (CAG→CGG) | yfjQ → | CP4‑57 prophage, uncharacterized protein |
| RA | 2,883,176 | T→C | 6.3% | N321D (AAT→GAT) | casA ← | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| JC | 2,977,560 | Δ33 bp | 34.7% | coding (964‑996/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor, autorepressor |
| RA | 3,194,978 | C→A | 6.9% | intergenic (‑115/+119) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,194,984 | A→T | 7.1% | intergenic (‑121/+113) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,194,985 | C→T | 7.0% | intergenic (‑122/+112) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,194,994 | G→A | 7.3% | intergenic (‑131/+103) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,195,006 | C→G | 7.1% | intergenic (‑143/+91) | sibD ← / ← sibE | sRNA antisense regulator of toxic IbsD protein/sRNA antisense regulator of toxic IbsE protein |
| RA | 3,489,896 | C→A | 5.4% | E95* (GAG→TAG) | argD ← | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,959,990 | T→A | 11.5% | intergenic (‑178/+21) | ppiC ← / ← yifN | peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/PemK toxin family pseudogene |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,160,112 | G→T | 100% | H226Q (CAC→CAA) | sthA ← | pyridine nucleotide transhydrogenase, soluble |
| RA | 4,160,853 | C→T | 100% | intergenic (‑64/‑270) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,246,287 | G→A | 5.1% | N44N (AAC→AAT) | malE ← | maltose transporter subunit |
| RA | 4,296,189 | A→G | 26.7% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 26.8% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 27.9% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,433,830 | C→T | 9.7% | V66M (GTG→ATG) | qorB ← | NAD(P)H:quinone oxidoreductase |
| RA | 4,577,406 | T→C | 4.5% | Y185C (TAC→TGC) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1812688 | 1812952 | 265 | 19 [17] | [16] 18 | ydjO | uncharacterized protein |
| * | * | ÷ | NC_000913 | 2103899 | 2104128 | 230 | 23 [17] | [17] 19 | wbbK | lipopolysaccharide biosynthesis protein |
| * | * | ÷ | NC_000913 | 3268864 | 3269652 | 789 | 19 [17] | [16] 18 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3423895–3424229 | 3424410–3424238 | 10–516 | 18 [17] | [17] 19 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 3653670 | 3653828 | 159 | 19 [17] | [17] 18 | [yhiS] | [yhiS] |
| * | * | ÷ | NC_000913 | 3796930 | 3797468 | 539 | 19 [16] | [17] 18 | [waaC]–[waaL] | [waaC], [waaL] |
| * | * | ÷ | NC_000913 | 3798868 | 3799593 | 726 | 18 [16] | [17] 18 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 3804230 | 3805233 | 1004 | 18 [13] | [15] 19 | [waaS]–[waaP] | [waaS], [waaP] |
| * | * | ÷ | NC_000913 | 4233682 | 4235847 | 2166 | 18 [16] | [15] 18 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 166404 = | 76 (1.300) | 6 (0.110) | 4/502 | NT | 8.3% | coding (1675/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase |
| ? | NC_000913 | 166643 = | 59 (1.040) | coding (1914/2535 nt) | mrcB | fused glycosyl transferase and transpeptidase | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 49 (0.840) | 43/518 | NT | 100% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 275149 | NA (NA) | 3 (0.050) | 3/518 | NT | 8.8% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | = 1109374 | 31 (0.530) | coding (40/1536 nt) | opgG | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase | |||||
| * | ? | NC_000913 | = 275988 | 42 (0.720) | 3 (0.050) | 3/504 | NT | 5.8% | coding (664/1404 nt) | mmuP | CP4‑6 prophage, putative S‑methylmethionine transporter |
| ? | NC_000913 | = 276355 | 56 (0.990) | coding (1031/1404 nt) | mmuP | CP4‑6 prophage, putative S‑methylmethionine transporter | |||||
| * | ? | NC_000913 | 689625 = | 55 (0.940) | 3 (0.050) | 3/502 | NT | 4.6% | coding (1257/1539 nt) | lnt | apolipoprotein N‑acyltransferase |
| ? | NC_000913 | 690143 = | 70 (1.240) | coding (739/1539 nt) | lnt | apolipoprotein N‑acyltransferase | |||||
| * | ? | NC_000913 | = 858176 | 84 (1.440) | 3 (0.050) | 3/500 | NT | 3.9% | coding (886/1266 nt) | ybiU | DUF1479 family protein |
| ? | NC_000913 | = 858343 | 65 (1.150) | coding (719/1266 nt) | ybiU | DUF1479 family protein | |||||
| * | ? | NC_000913 | = 933725 | 50 (0.860) | 3 (0.050) | 3/506 | NT | 5.7% | coding (502/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes |
| ? | NC_000913 | = 933736 | 50 (0.880) | coding (513/3990 nt) | ftsK | DNA translocase at septal ring sorting daughter chromsomes | |||||
| * | ? | NC_000913 | 1110158 = | 42 (0.720) | 12 (0.210) | 12/516 | NT | 22.3% | coding (824/1536 nt) | opgG | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| ? | NC_000913 | = 1469239 | NA (NA) | intergenic (‑90/‑2) | insC1/ydbA | IS2 repressor TnpA/pseudogene, autotransporter homolog, interrupted by IS2 and IS30 | |||||
| * | ? | NC_000913 | = 1110164 | 42 (0.720) | 28 (0.480) | 24/516 | NT | 40.1% | coding (830/1536 nt) | opgG | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| ? | NC_000913 | = 1651547 | NA (NA) | intergenic (+10/‑4) | insD1/intQ | IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/pseudogene, Qin prophage, phage integrase family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.290) | 28 (0.510) | 24/486 | NT | 63.0% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.270) | 38 (0.690) | 33/486 | NT | 70.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 53 (0.910) | 44/518 | NT | 100% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1404200 | 58 (0.990) | 3 (0.050) | 3/504 | NT | 4.5% | coding (366/1311 nt) | abgA | p‑aminobenzoyl‑glutamate hydrolase, A subunit |
| ? | NC_000913 | = 1404415 | 70 (1.230) | coding (151/1311 nt) | abgA | p‑aminobenzoyl‑glutamate hydrolase, A subunit | |||||
| * | ? | NC_000913 | 1932802 = | 48 (0.820) | 53 (0.910) | 39/514 | NT | 51.8% | coding (1803/1812 nt) | edd | 6‑phosphogluconate dehydratase |
| ? | NC_000913 | = 1969467 | 51 (0.880) | coding (1518/1602 nt) | tap | methyl‑accepting protein IV | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 18 (0.310) | 15/518 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 39 (0.670) | 31/518 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | 2514275 = | NA (NA) | 56 (0.970) | 41/512 | NT | 95.0% | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| ? | NC_000913 | = 2536318 | 3 (0.050) | coding (487/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | = 2515612 | NA (NA) | 48 (0.830) | 38/514 | NT | 96.0% | intergenic (+171/+29) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase |
| ? | NC_000913 | 2536308 = | 2 (0.030) | coding (477/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | = 2570109 | 61 (1.040) | 4 (0.070) | 4/492 | NT | 8.5% | coding (227/837 nt) | eutJ | ethanolamine utilization protein, HSP70/actin superfamily protein |
| ? | NC_000913 | = 2570314 | 28 (0.510) | coding (22/837 nt) | eutJ | ethanolamine utilization protein, HSP70/actin superfamily protein | |||||
| * | ? | NC_000913 | = 2883759 | 57 (0.980) | 3 (0.050) | 3/510 | NT | 5.0% | coding (378/1509 nt) | casA | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| ? | NC_000913 | = 2883890 | 59 (1.030) | coding (247/1509 nt) | casA | CRISP RNA (crRNA) containing Cascade antiviral complex protein | |||||
| * | ? | NC_000913 | = 3841540 | 28 (0.480) | 3 (0.050) | 3/508 | NT | 6.2% | coding (199/1191 nt) | nepI | putative transporter |
| ? | NC_000913 | = 3842378 | 63 (1.100) | coding (24/453 nt) | yicN | DUF1198 family protein | |||||