mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 29,987 | A→T | 5.4% | I113F (ATC→TTC) | carA → | carbamoyl phosphate synthetase small subunit, glutamine amidotransferase |
| RA | 171,836 | C→T | 5.6% | V81V (GTC→GTT) | clcA → | H(+)/Cl(‑) exchange transporter |
| RA | 568,077 | C→T | 5.5% | H52H (CAC→CAT) | ybcN → | DLP12 prophage; uncharacterized protein |
| RA | 844,648 | Δ1 bp | 5.1% | intergenic (‑281/+18) | dps ← / ← rhtA | Fe‑binding and storage protein; stress‑inducible DNA‑binding protetin/threonine and homoserine efflux system |
| RA | 1,083,475 | C→A | 6.8% | W613C (TGG→TGT) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,380,931 | T→A | 5.5% | intergenic (+102/‑46) | ycjF → / → tyrR | UPF0283 family inner membrane protein/aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| RA | 1,384,589 | C→A | 6.6% | R89R (CGG→CGT) | mpaA ← | murein peptide amidase A |
| RA | 1,391,508 | T→C | 5.3% | intergenic (+159/‑114) | insH1 → / → ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| RA | 1,391,511 | G→A | 5.3% | intergenic (+162/‑111) | insH1 → / → ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| RA | 1,555,519 | T→A | 5.4% | D407V (GAC→GTC) | ddpA ← | D‑ala‑D‑a la transporter subunit |
| RA | 1,578,186 | T→A | 6.4% | T11S (ACG→TCG) | safA ← | two‑component system connector membrane protein, EvgSA to PhoQP |
| RA | 1,581,513 | A→T | 6.2% | L160* (TTA→TAA) | ydeQ ← | putative fimbrial‑like adhesin protein |
| RA | 1,589,995 | Δ1 bp | 5.4% | pseudogene (2250/5323 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,636,462 | A→T | 5.0% | intergenic (+138/+284) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,467 | A→T | 5.0% | intergenic (+143/+279) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,766,063 | T→A | 6.5% | S246T (TCG→ACG) | ydiM → | MFS superfamily sugar transport 1 family protein |
| RA | 1,866,468 | T→A | 5.2% | N57K (AAT→AAA) | yeaJ → | putative diguanylate cyclase |
| RA | 1,897,871 | T→C | 5.1% | V178A (GTG→GCG) | manY → | mannose‑specific enzyme IIC component of PTS |
| RA | 1,956,275 | C→A | 8.0% | A16D (GCT→GAT) | yecT → | uncharacterized protein |
| RA | 2,294,921 | G→A | 6.6% | H438Y (CAC→TAC) | napA ← | nitrate reductase, periplasmic, large subunit |
| RA | 2,399,955 | C→A | 100% | E56* (GAA→TAA) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,765,989 | C→T | 5.0% | pseudogene (437/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage;Phage or Prophage Related; putative pump protein |
| RA | 2,800,152 | C→A | 5.3% | P262T (CCG→ACG) | proW → | glycine betaine transporter subunit |
| RA | 2,939,863 | A→T | 5.9% | D225E (GAT→GAA) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 3,406,964 | C→T | 5.1% | intergenic (‑140/‑259) | acrS ← / → acrE | acrAB operon transcriptional repressor/cytoplasmic membrane lipoprotein |
| RA | 3,425,043 | G→A | 6.7% | T93T (ACC→ACT) | yrdD ← | putative DNA topoisomerase |
| RA | 3,467,158 | G→A | 6.4% | R95C (CGT→TGT) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,910,484 | A→T | 5.1% | T84T (ACT→ACA) | atpD ← | F1 sector of membrane‑bound ATP synthase, beta subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 2208269 | 2209125 | 857 | 46 [45] | [45] 47 | mlrA | mlrA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 270239 = | NA (NA) | 3 (0.030) | 3/256 | NT | NA | noncoding (34/335 nt) | IS911 | repeat region |
| ? | CP009273 | 270302 = | NA (NA) | noncoding (97/335 nt) | IS911 | repeat region | |||||
| * | ? | CP009273 | 360104 = | 79 (0.840) | 144 (1.520) | 99/266 | NT | 64.6% | 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 | = 366870 | NA (NA) | 4 (0.040) | 4/250 | NT | NA | noncoding (880/1223 nt) | IS30 | repeat region |
| ? | CP009273 | = 366962 | NA (NA) | noncoding (972/1223 nt) | IS30 | repeat region | |||||
| * | ? | CP009273 | = 387196 | 55 (0.580) | 4 (0.040) | 4/256 | NT | 8.3% | noncoding (1227/1258 nt) | IS3 | repeat region |
| ? | CP009273 | 563424 = | 36 (0.400) | coding (831/867 nt) | insF1 | IS3 transposase B | |||||
| * | ? | CP009273 | = 579689 | 84 (0.890) | 7 (0.080) | 6/256 | NT | 8.4% | coding (553/750 nt) | appY | global transcriptional activator; DLP12 prophage |
| ? | CP009273 | = 579743 | 72 (0.790) | coding (607/750 nt) | appY | global transcriptional activator; DLP12 prophage | |||||
| * | ? | CP009273 | = 790231 | 65 (0.690) | 4 (0.040) | 4/254 | NT | 5.7% | coding (3/150 nt) | acrZ | AcrAB‑TolC efflux pump accessory protein, membrane‑associated |
| ? | CP009273 | = 790266 | 70 (0.770) | coding (38/150 nt) | acrZ | AcrAB‑TolC efflux pump accessory protein, membrane‑associated | |||||
| * | ? | CP009273 | 1059218 = | 89 (0.940) | 6 (0.070) | 4/256 | NT | 6.6% | coding (14/921 nt) | cbpA | DnaK co‑chaperone; curved DNA‑binding protein |
| ? | CP009273 | 1059268 = | 85 (0.930) | intergenic (‑37/‑224) | cbpA/yccE | DnaK co‑chaperone; curved DNA‑binding protein/uncharacterized protein | |||||
| * | ? | CP009273 | = 1108887 | 105 (1.160) | 7 (0.080) | 5/254 | NT | 6.2% | noncoding (15/98 nt) | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | CP009273 | = 1108950 | NA (NA) | noncoding (78/98 nt) | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP97 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | 1203246 = | 35 (0.370) | 39 (0.470) | 33/234 | NT | 52.1% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 41 (0.490) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 34 (0.360) | 47 (0.560) | 39/234 | NT | 57.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 41 (0.490) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1210749 = | 53 (0.560) | 3 (0.030) | 3/264 | NT | 5.2% | coding (183/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| ? | CP009273 | 1210800 = | 56 (0.600) | coding (132/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP | |||||
| * | ? | CP009273 | 1210751 = | 53 (0.560) | 4 (0.040) | 4/252 | NT | 7.0% | coding (181/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| ? | CP009273 | 1210798 = | 56 (0.620) | coding (134/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP | |||||
| * | ? | CP009273 | = 1210757 | 56 (0.590) | 3 (0.030) | 3/252 | NT | 5.2% | coding (175/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP |
| ? | CP009273 | = 1210790 | 56 (0.620) | coding (142/1212 nt) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP | |||||
| * | ? | CP009273 | 1406910 = | 79 (0.840) | 5 (0.060) | 3/250 | NT | 6.4% | coding (583/1236 nt) | intR | Rac prophage; integrase |
| ? | CP009273 | 1406987 = | 73 (0.820) | coding (506/1236 nt) | intR | Rac prophage; integrase | |||||
| * | ? | CP009273 | 1428167 = | NA (NA) | 3 (0.030) | 3/260 | NT | 25.4% | intergenic (‑236/+81) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage |
| ? | CP009273 | 1428195 = | 9 (0.100) | intergenic (‑264/+53) | pinR/ynaE | Rac prophage; putative site‑specific recombinase/cold shock protein, Rac prophage | |||||
| * | ? | CP009273 | = 1573633 | 55 (0.580) | 4 (0.040) | 4/250 | NT | 5.4% | intergenic (‑34/+257) | yddA/ydeM | putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component/putative YdeN‑specific sulfatase‑maturating enzyme |
| ? | CP009273 | = 1573730 | 88 (0.990) | intergenic (‑131/+160) | yddA/ydeM | putative multidrug transporter subunit of ABC superfamily, membrane component/ATP‑binding component/putative YdeN‑specific sulfatase‑maturating enzyme | |||||
| * | ? | CP009273 | 2599729 = | 80 (0.850) | 5 (0.050) | 3/260 | NT | 5.8% | coding (109/651 nt) | hyfE | hydrogenase 4, membrane subunit |
| ? | CP009273 | 2599774 = | 83 (0.900) | coding (154/651 nt) | hyfE | hydrogenase 4, membrane subunit | |||||
| * | ? | CP009273 | = 2724587 | 7 (0.070) | 3 (0.030) | 3/252 | NT | 31.1% | intergenic (‑71/+372) | rrsG/clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| ? | CP009273 | 4028859 = | NA (NA) | intergenic (+346/‑32) | hemG/rrsA | protoporphyrin oxidase, flavoprotein/16S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 2962916 = | 91 (0.960) | 5 (0.050) | 5/260 | NT | 5.3% | intergenic (‑580/‑105) | rppH/mutH | RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein |
| ? | CP009273 | 2962997 = | 91 (0.980) | intergenic (‑661/‑24) | rppH/mutH | RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein | |||||
| * | ? | CP009273 | = 4224327 | 72 (0.760) | 6 (0.070) | 4/252 | NT | 7.2% | coding (642/1650 nt) | pgi | glucosephosphate isomerase |
| ? | CP009273 | = 4224360 | 86 (0.960) | coding (675/1650 nt) | pgi | glucosephosphate isomerase | |||||
| * | ? | CP009273 | 4532499 = | 90 (0.950) | 12 (0.140) | 12/248 | NT | 12.6% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 82 (0.930) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 4532507 | 88 (0.930) | 10 (0.110) | 8/248 | NT | 10.9% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 82 (0.930) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||