mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 264,098 | G→T | 100% | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | 100% | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 333,465 | A→G | 5.7% | intergenic (+6/+36) | yahA → / ← yahB | c‑di‑GMP‑specific phosphodiesterase/putative DNA‑bindng transcriptional regulator |
| RA | 372,055 | C→A | 6.8% | H273N (CAT→AAT) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase |
| RA | 482,230 | G→A | 100% | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 871,104 | G→T | 8.0% | Q46H (CAG→CAT) | gsiC → | glutathione ABC transporter permease |
| RA | 1,026,965 | C→G | 12.2% | V17V (GTG→GTC) | mgsA ← | methylglyoxal synthase |
| RA | 1,051,638 | C→T | 9.4% | R60C (CGT→TGT) | cspG → | cold shock protein homolog, cold‑inducible |
| RA | 1,197,502 | C→T | 100% | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,494,281 | G→T | 7.3% | A264D (GCC→GAC) | ydcI ← | putative DNA‑binding transcriptional regulator |
| RA | 1,544,022 | 1 bp→AA | 100% | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,933,131 | G→A | 8.9% | P492S (CCG→TCG) | edd ← | 6‑phosphogluconate dehydratase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | 100% | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,172,505 | A→T | 6.2% | V123V (GTT→GTA) | gatD ← | galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| 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 | 2,355,843 | T→C | 9.4% | F108S (TTC→TCC) | glpC → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, C subunit, 4Fe‑4S iron‑sulfur cluster |
| RA | 2,384,151 | C→T | 7.4% | G524G (GGG→GGA) | yfbK ← | Von Willebrand factor domain putative lipoprotein |
| RA | 2,391,417 | C→G | 8.3% | W30S (TGG→TCG) | nuoN ← | NADH:ubiquinone oxidoreductase, membrane subunit N |
| RA | 2,679,525 | G→T | 100% | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | 100% | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | 100% | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,440,923 | C→T | 49.7% | G36D (GGC→GAC) | rpoA ← | RNA polymerase, alpha subunit |
| 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 | 3,591,716 | A→G | 7.6% | W204R (TGG→CGG) | ugpB ← | sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,698,796 | C→T | 9.0% | P195S (CCC→TCC) | bcsG → | DUF3260 family cellulose production inner membrane protein |
| RA | 4,032,422 | G→A | 5.7% | R421H (CGT→CAT) | pepQ → | proline dipeptidase |
| RA | 4,111,596 | G→A | 100% | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| RA | 4,186,457 | A→G | 45.3% | K398E (AAG→GAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,295,976 | C→T | 21.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,296:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,545,683 | C→A | 7.8% | D224E (GAC→GAA) | fimD → | fimbrial usher outer membrane porin protein; FimCD chaperone‑usher |
| RA | 4,604,632 | C→A | 100% | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 5565 = | NA (NA) | 3 (0.060) | 3/258 | NT | NA | noncoding (1/105 nt) | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_tpiA | 5597 = | NA (NA) | noncoding (33/105 nt) | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP1 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_tpiA | 948822 = | 36 (0.690) | 4 (0.080) | 4/258 | NT | 10.8% | coding (747/909 nt) | ycaN | LysR family putative transcriptional regulator |
| ? | NC_000913_3_pae_tpiA | 948840 = | 32 (0.650) | coding (729/909 nt) | ycaN | LysR family putative transcriptional regulator | |||||
| * | ? | NC_000913_3_pae_tpiA | 1207790 = | 4 (0.080) | 33 (0.720) | 30/240 | NT | 84.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | 1209619 = | 9 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1207805 | 3 (0.060) | 38 (0.830) | 31/240 | NT | 86.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | = 1209602 | 9 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1299498 | 0 (0.000) | 39 (0.770) | 32/264 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_pae_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_pae_tpiA | 2769787 = | 67 (1.290) | 3 (0.060) | 3/252 | NT | 5.1% | coding (85/702 nt) | yfjR | CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| ? | NC_000913_3_pae_tpiA | 2769834 = | 50 (1.040) | coding (132/702 nt) | yfjR | CP4‑57 prophage; putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913_3_pae_tpiA | 4122239 = | 55 (1.060) | 3 (0.060) | 3/256 | NT | 5.5% | intergenic (‑36/+57) | hslV/ftsN | peptidase component of the HslUV protease/essential cell division protein |
| ? | NC_000913_3_pae_tpiA | 4122259 = | 52 (1.060) | intergenic (‑56/+37) | hslV/ftsN | peptidase component of the HslUV protease/essential cell division protein | |||||