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 |
| RA | 7,286 | A→G | 5.3% | M225T (ATG→ACG) | yaaJ ← | putative transporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 962,982 | G→C | 22.7% | V330L (GTT→CTT) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,020,956 | A→G | 32.8% | intergenic (‑37/‑182) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,677,913 | T→C | 61.4% | intergenic (‑10/‑514) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,292,159 | C→T | 5.2% | V84V (GTG→GTA) | ccmH ← | heme lyase, CcmH subunit |
| RA | 2,912,203 | Δ1 bp | 8.0% | coding (1449/2235 nt) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,912,636 | C→T | 15.2% | R339H (CGC→CAC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 3,233,246 | T→G | 5.1% | F528V (TTC→GTC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| 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 |
| JC JC | 3,578,758 | IS5 (–) +4 bp | 29.6% | intergenic (‑32/+189) | gntR ← / ← yhhW | d‑gluconate inducible gluconate regulon transcriptional repressor/quercetinase activity in vitro |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,190 | A→G | 26.6% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 29.0% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 20.1% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 10.7% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,346,816 | A→T | 5.4% | Y171N (TAC→AAC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2099630 | 2101384 | 1755 | 43 [40] | [31] 43 | gnd | gnd |
| * | * | ÷ | NC_000913 | 3423816–3424430 | 3424430 | 1–615 | 41 [40] | [40] 41 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 227039 | 54 (0.560) | 3 (0.030) | 3/510 | NT | 5.3% | noncoding (1281/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 227046 | 54 (0.570) | noncoding (1288/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | 1207790 = | 32 (0.330) | 41 (0.450) | 33/490 | NT | 57.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 31 (0.340) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.320) | 55 (0.600) | 43/490 | NT | 64.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 31 (0.340) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 44 (0.460) | 37/514 | 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 | = 3498081 | 90 (0.930) | 5 (0.050) | 5/504 | NT | 5.3% | coding (254/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase |
| ? | NC_000913 | = 3498086 | 91 (0.970) | coding (259/1374 nt) | cysG | fused siroheme synthase 1,3‑dimethyluroporphyriongen III dehydrogenase and siroheme ferrochelatase/uroporphyrinogen methyltransferase | |||||