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 | 32,767 | Δ1 bp | 5.5% | coding (1951/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 32,768 | Δ1 bp | 5.5% | coding (1952/3222 nt) | carB → | carbamoyl‑phosphate synthase large subunit |
| RA | 202,876 | Δ1 bp | 6.3% | coding (317/789 nt) | lpxA → | UDP‑N‑acetylglucosamine acetyltransferase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 463,704 | Δ1 bp | 5.6% | coding (1790/1872 nt) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 463,705 | Δ1 bp | 5.6% | coding (1791/1872 nt) | ppiD → | periplasmic folding chaperone, has an inactive PPIase domain |
| RA | 711,536 | C→T | 100% | intergenic (‑71/+69) | fldA ← / ← ybfE | flavodoxin 1/LexA‑regulated protein, CopB family |
| RA | 756,349 | C→T | 5.1% | T148M (ACG→ATG) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| RA | 1,164,976 | G→A | 6.1% | P294P (CCG→CCA) | nagZ → | beta N‑acetyl‑glucosaminidase |
| RA | 1,196,305 | C→T | 100% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| 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 | 1,365,853 | G→A | 4.7% | A102T (GCC→ACC) | puuE → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 1,648,197 | A→T | 8.6% | K88N (AAA→AAT) | dicA → | Qin prophage, putative regulator for DicB |
| RA | 1,722,169 | A→G | 6.1% | T17A (ACG→GCG) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| 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 | 2,304,520 | G→T | 10.5% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,521 | G→C | 16.6% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,535 | A→G | 18.5% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,459,579:1 | +G | 6.2% | coding (889/1311 nt) | fadI ← | beta‑ketoacyl‑CoA thiolase, anaerobic, subunit |
| JC | 2,533,399 | Δ10 bp | 47.9% | intergenic (+21/‑354) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,759,638 | T→C | 10.3% | L219S (TTA→TCA) | yfjI → | CP4‑57 prophage, uncharacterized protein |
| RA | 2,818,282 | C→T | 9.8% | intergenic (‑10/+189) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,286 | C→T | 9.8% | intergenic (‑14/+185) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,295 | A→T | 9.2% | intergenic (‑23/+176) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,301 | T→A | 8.9% | intergenic (‑29/+170) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,818,322 | G→A | 9.1% | intergenic (‑50/+149) | argY ← / ← argV | tRNA‑Arg/tRNA‑Arg |
| RA | 2,819,347 | A→G | 6.3% | intergenic (‑203/+32) | csrA ← / ← alaS | pleiotropic regulatory protein for carbon source metabolism/alanyl‑tRNA synthetase |
| RA | 3,159,528 | G→A | 5.4% | G539G (GGC→GGT) | ygiQ ← | Radical SAM superfamily protein |
| JC | 3,213,568 | Δ48 bp | 45.7% | coding (524‑571/1842 nt) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,683,940 | Δ1 bp | 4.9% | coding (1678/1989 nt) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| 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 | 4,076,021 | C→G | 5.9% | S157* (TCA→TGA) | yihX → | alpha‑D‑glucose‑1‑phosphate phosphatase, anomer‑specific |
| RA | 4,153,569 | G→A | 5.8% | intergenic (‑472/+126) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,594 | A→C | 8.1% | intergenic (‑497/+101) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,153,615 | C→T | 7.4% | intergenic (‑518/+80) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,246,254 | T→C | 7.0% | K55K (AAA→AAG) | malE ← | maltose transporter subunit |
| RA | 4,296,267 | T→C | 27.3% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,326,242 | C→T | 6.8% | intergenic (‑500/+158) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,248 | C→T | 8.9% | intergenic (‑506/+152) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,560,883 | A→T | 6.4% | intergenic (‑202/‑48) | yjiH ← / → kptA | nucleoside recognition pore and gate family putative inner membrane transporter/RNA 2'‑phosphotransferase |
| RA | 4,625,882 | T→G | 5.7% | intergenic (+18/‑31) | serB → / → radA | 3‑phosphoserine phosphatase/DNA repair protein |
| RA | 4,633,013 | G→A | 4.1% | G85R (GGA→AGA) | trpR → | transcriptional repressor, tryptophan‑binding |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423898–3424228 | 3424406–3424240 | 13–509 | 16 [15] | [15] 16 | rrlD | 23S ribosomal RNA of rrnD operon |
| * | * | ÷ | NC_000913 | 4233766 | 4235410 | 1645 | 16 [15] | [15] 16 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 58 (1.010) | 47/510 | 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 | 411642 = | 51 (0.890) | 3 (0.050) | 3/494 | NT | 6.0% | coding (840/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family |
| ? | NC_000913 | 411680 = | 44 (0.790) | coding (802/1185 nt) | araJ | L‑arabinose‑inducible putative transporter, MFS family | |||||
| * | ? | NC_000913 | 458787 = | 3 (0.050) | 37 (0.660) | 32/504 | NT | 92.6% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 1 (0.020) | 66 (1.170) | 50/502 | NT | 98.5% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 608011 = | NA (NA) | 21 (0.370) | 15/502 | NT | 40.8% | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase |
| ? | NC_000913 | 1259756 = | 31 (0.540) | coding (1048/1680 nt) | dauA | C4‑dicarboxylic acid transporter | |||||
| * | ? | NC_000913 | = 609347 | NA (NA) | 15 (0.270) | 15/504 | NT | 32.9% | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex |
| ? | NC_000913 | = 1259767 | 31 (0.540) | coding (1037/1680 nt) | dauA | C4‑dicarboxylic acid transporter | |||||
| * | ? | NC_000913 | 1207790 = | 15 (0.260) | 31 (0.580) | 26/478 | NT | 68.8% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 14 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.260) | 33 (0.620) | 27/478 | NT | 70.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 14 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 0 (0.000) | 49 (0.860) | 38/510 | 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 | 1979486 = | 0 (0.000) | 22 (0.380) | 19/510 | 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 (0.680) | 31/510 | 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 | 2288917 = | NA (NA) | 43 (0.750) | 37/510 | NT | 89.6% | intergenic (‑5/+146) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 4049893 | 5 (0.090) | intergenic (+142/‑5) | polA/spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||
| * | ? | NC_000913 | = 2290111 | NA (NA) | 58 (1.010) | 46/510 | NT | 92.1% | 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 | 4049890 = | 5 (0.090) | intergenic (+139/‑8) | polA/spf | 5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease/Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||
| * | ? | NC_000913 | = 2729777 | 16 (0.280) | 4 (0.070) | 4/494 | NT | 20.5% | noncoding (1379/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon |
| ? | NC_000913 | = 2730008 | NA (NA) | noncoding (1148/1542 nt) | rrsG | 16S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913 | = 3714866 | 64 (1.120) | 4 (0.070) | 4/492 | NT | 6.6% | coding (1528/2334 nt) | bisC | biotin sulfoxide reductase |
| ? | NC_000913 | = 3715051 | 52 (0.940) | coding (1343/2334 nt) | bisC | biotin sulfoxide reductase | |||||
| * | ? | NC_000913 | 4317848 = | 78 (1.360) | 4 (0.070) | 4/490 | NT | 5.9% | coding (49/681 nt) | phnL | ribophosphonate triphosphate synthase subunit, putative ABC transporter‑related ATPase |
| ? | NC_000913 | 4318122 = | 53 (0.970) | coding (644/759 nt) | phnK | carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding protein | |||||
| * | ? | NC_000913 | = 4625876 | 64 (1.120) | 3 (0.050) | 3/496 | NT | 4.7% | intergenic (+12/‑37) | serB/radA | 3‑phosphoserine phosphatase/DNA repair protein |
| ? | NC_000913 | = 4625882 | 60 (1.080) | intergenic (+18/‑31) | serB/radA | 3‑phosphoserine phosphatase/DNA repair protein | |||||