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 | 31,320 | Δ1 bp | 2.6% | coding (504/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 48,346 | T→G | 14.2% | V193G (GTG→GGG) | kefC → | potassium:proton antiporter |
| RA | 71,870 | A→G | 7.5% | S174G (AGC→GGC) | yabI → | DedA family inner membrane protein |
| RA | 153,892 | Δ1 bp | 2.7% | coding (1535/2598 nt) | htrE ← | putative outer membrane usher protein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,176 | A→G | 10.9% | intergenic (+295/‑283) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 954,979 | C→T | 4.3% | G552S (GGC→AGC) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor |
| RA | 993,853 | G→A | 3.3% | T64T (ACC→ACT) | ssuB ← | aliphatic sulfonate ABC transporter ATPase |
| RA | 1,245,959 | G→A | 3.7% | A473V (GCG→GTG) | treA ← | periplasmic trehalase |
| RA | 1,446,816 | Δ1 bp | 3.8% | coding (468/906 nt) | feaR ← | transcriptional activator for tynA and feaB |
| RA | 1,603,740 | A→G | 14.9% | E241G (GAG→GGG) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,616,595 | C→A | 4.5% | P278H (CCT→CAT) | yneK → | uncharacterized protein |
| RA | 1,708,718 | G→A | 13.7% | A600A (GCG→GCA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,842,914 | A→G | 11.0% | M182V (ATG→GTG) | gdhA → | glutamate dehydrogenase, NADP‑specific |
| RA | 1,873,092 | G→A | 3.6% | G351E (GGA→GAA) | yeaJ → | putative diguanylate cyclase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,032,768 | A→G | 3.3% | I104I (ATT→ATC) | yedJ ← | putative HD superfamily phosphohydrolase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,162,421 | Δ1 bp | 3.1% | coding (958/1416 nt) | iceT → | putative citrate/iron‑citrate/zinc‑citrate efflux transporter |
| RA | 2,301,361 | Δ1 bp | 2.8% | coding (1391/2487 nt) | napA ← | nitrate reductase, periplasmic, large subunit |
| RA | 2,528,973 | T→C | 10.9% | E401G (GAG→GGG) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 2,817,989 | A→C | 8.5% | intergenic (‑131/+68) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,817,995 | A→G | 8.0% | intergenic (‑137/+62) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,009 | A→T | 5.7% | intergenic (‑151/+48) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,011 | T→A | 6.7% | intergenic (‑153/+46) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,969,474 | T→C | 6.1% | intergenic (‑499/‑186) | rppH ← / → mutH | RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein |
| RA | 3,233,183 | T→G | 14.4% | G507G (GGT→GGG) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,495,036 | C→A | 10.6% | A343E (GCA→GAA) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| RA | 3,630,509 | A→C | 15.3% | G31G (GGT→GGG) | yhiI ← | putative membrane fusion protein (MFP) of efflux pump |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,052,347 | G→A | 2.8% | G102R (GGG→AGG) | hemN → | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| RA | 4,123,275 | A→G | 8.8% | S22P (TCA→CCA) | ftsN ← | essential cell division protein |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,292,123 | A→G | 10.0% | I205V (ATC→GTC) | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| RA | 4,295,833 | T→C | 5.1% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 5.9% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 20.1% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 28.7% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,332,310 | A→C | 10.6% | L322V (TTA→GTA) | basS ← | sensory histidine kinase in two‑component regulatory system with BasR |
| RA | 4,442,797 | Δ1 bp | 3.7% | coding (415/1734 nt) | tamA → | translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,509,781 | C→T | 2.6% | pseudogene (302/315 nt) | insO → | pseudogene, IS911 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 124 (1.110) | 76/502 | 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 | = 365932 | 111 (0.990) | 4 (0.040) | 4/486 | NT | 3.8% | coding (374/3075 nt) | lacZ | beta‑D‑galactosidase |
| ? | NC_000913 | = 366332 | 95 (0.880) | intergenic (‑27/+96) | lacZ/lacI | beta‑D‑galactosidase/lactose‑inducible lac operon transcriptional repressor | |||||
| * | ? | NC_000913 | 762116 = | 134 (1.200) | 4 (0.040) | 3/474 | NT | 3.2% | coding (595/1218 nt) | sucB | dihydrolipoyltranssuccinase |
| ? | NC_000913 | 762340 = | 116 (1.100) | coding (819/1218 nt) | sucB | dihydrolipoyltranssuccinase | |||||
| * | ? | NC_000913 | 1207790 = | 27 (0.240) | 59 (0.560) | 47/470 | NT | 74.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.140) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.240) | 83 (0.790) | 56/470 | NT | 80.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.140) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1272758 = | 110 (0.990) | 5 (0.050) | 5/480 | NT | 4.9% | coding (252/696 nt) | chaC | cation transport regulator |
| ? | NC_000913 | 1273352 = | 90 (0.840) | coding (248/354 nt) | ychN | putative sulfur relay protein | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.030) | 117 (1.050) | 74/502 | NT | 97.5% | 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 | = 1299498 | 0 (0.000) | 53 (0.480) | 38/494 | 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 | 1899106 = | 133 (1.190) | 3 (0.030) | 3/484 | NT | 2.5% | coding (680/1599 nt) | yoaD | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| ? | NC_000913 | 1899503 = | 104 (0.970) | coding (1077/1599 nt) | yoaD | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 54 (0.480) | 43/502 | 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) | 87 (0.780) | 62/502 | 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 | = 2348718 | 116 (1.040) | 3 (0.030) | 3/492 | NT | 2.6% | coding (207/255 nt) | yfaE | ferredoxin involved with ribonucleotide reductase diferric‑tyrosyl radical (Y*) cofactor maintenance |
| ? | NC_000913 | = 2349188 | 107 (0.980) | coding (283/651 nt) | inaA | acid‑inducible Kdo/WaaP family putative kinase | |||||
| * | ? | NC_000913 | = 2489845 | 72 (0.640) | 4 (0.040) | 4/490 | NT | 6.5% | coding (340/945 nt) | yfdV | putative transporter |
| ? | NC_000913 | = 2490758 | 45 (0.410) | coding (1191/1695 nt) | oxc | oxalyl CoA decarboxylase, ThDP‑dependent | |||||
| * | ? | NC_000913 | = 2707461 | 120 (1.070) | 6 (0.060) | 3/490 | NT | 5.2% | coding (339/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component |
| ? | NC_000913 | = 2707648 | 101 (0.930) | coding (152/480 nt) | rseC | SoxR iron‑sulfur cluster reduction factor component | |||||
| * | ? | NC_000913 | 3090224 = | 123 (1.100) | 3 (0.030) | 3/494 | NT | 2.7% | coding (472/498 nt) | yggI | Zn‑dependent metalloprotease‑related protein |
| ? | NC_000913 | 3090936 = | 97 (0.880) | coding (592/708 nt) | endA | DNA‑specific endonuclease I | |||||
| * | ? | NC_000913 | 3463080 = | 96 (0.860) | 6 (0.050) | 5/492 | NT | 6.2% | coding (159/984 nt) | gspK | general secretory pathway component, cryptic |
| ? | NC_000913 | 3463294 = | 87 (0.800) | coding (373/984 nt) | gspK | general secretory pathway component, cryptic | |||||
| * | ? | NC_000913 | = 3727556 | 105 (0.940) | 6 (0.060) | 4/486 | NT | 7.2% | coding (192/342 nt) | yiaB | YiaAB family inner membrane protein |
| ? | NC_000913 | = 3727755 | 52 (0.480) | intergenic (‑8/+161) | yiaB/xylB | YiaAB family inner membrane protein/xylulokinase | |||||
| * | ? | NC_000913 | = 4059965 | 105 (0.940) | 4 (0.040) | 3/484 | NT | 4.1% | coding (1560/1824 nt) | typA | GTP‑binding protein |
| ? | NC_000913 | = 4060164 | 84 (0.780) | coding (1759/1824 nt) | typA | GTP‑binding protein | |||||
| * | ? | NC_000913 | = 4265211 | 141 (1.260) | 5 (0.050) | 4/488 | NT | 3.2% | coding (899/1416 nt) | dnaB | replicative DNA helicase |
| ? | NC_000913 | = 4265440 | 168 (1.550) | coding (1128/1416 nt) | dnaB | replicative DNA helicase | |||||
| * | ? | NC_000913 | 4280995 = | 129 (1.160) | 6 (0.060) | 6/480 | NT | 4.2% | coding (1017/1650 nt) | yjcE | putative cation/proton antiporter |
| ? | NC_000913 | 4281528 = | 150 (1.410) | coding (1550/1650 nt) | yjcE | putative cation/proton antiporter | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 11 (0.120) | 5/424 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913 | 4542683 = | 21 (0.190) | 11 (0.100) | 11/484 | NT | 26.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542997 = | 41 (0.380) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913 | = 4542691 | 20 (0.180) | 9 (0.080) | 8/484 | NT | 23.0% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | = 4542987 | 41 (0.380) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||