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 | annotation | gene | description |
| RA | 202,398 | C→T | R100C (CGC→TGC) | fabZ → | (3R)‑hydroxymyristol acyl carrier protein dehydratase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| MC JC | 1,678,015 | Δ73 bp | intergenic (‑112/‑340) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,731,621 | G→T | M845I (ATG→ATT) | lhr → | putative ATP‑dependent helicase |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,867,401 | Δ1 bp | coding (151/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 3,440,176 | G→A | T285I (ACC→ATC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,560,455 | +G | 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 | 4,234,667 | Δ1 bp | intergenic (‑1434/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,295,641 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_pae_pgi | 366321 | 366347 | 27 | 3 [2] | [1] 3 | lacZ/lacI | beta‑D‑galactosidase/lactose‑inducible lac operon transcriptional repressor |
| * | * | ÷ | NC_000913_3_pae_pgi | 1528456–1529173 | 1529289 | 117–834 | 3 [2] | [2] 3 | rhsE | pseudogene, Rhs family |
| * | * | ÷ | NC_000913_3_pae_pgi | 3423755–3424234 | 3424522–3424238 | 5–768 | 3 [2] | [2] 3 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 81852 | 11 (0.630) | 5 (0.300) | 4/260 | 1.8 | 32.8% | coding (107/1092 nt) | leuB | 3‑isopropylmalate dehydrogenase, NAD(+)‑dependent |
| ? | NC_000913_3_pae_pgi | = 81864 | 10 (0.600) | coding (95/1092 nt) | leuB | 3‑isopropylmalate dehydrogenase, NAD(+)‑dependent | |||||
| * | ? | NC_000913_3_pae_pgi | = 228108 | NA (NA) | 8 (0.480) | 7/264 | 1.1 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_pgi | 349791 = | 7 (0.400) | 5 (0.300) | 5/258 | 1.5 | 40.6% | noncoding (187/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences |
| ? | NC_000913_3_pae_pgi | 349823 = | 8 (0.490) | noncoding (219/365 nt) | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | REP25 (repetitive extragenic palindromic) element; contains 8 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | 730954 = | 15 (0.870) | 4 (0.240) | 4/260 | 1.8 | 21.8% | coding (1372/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913_3_pae_pgi | 3620588 = | NA (NA) | coding (1397/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913_3_pae_pgi | = 1207805 | 7 (0.400) | 12 (0.790) | 12/240 | 0.4 | 74.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | = 1209602 | 2 (0.130) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 1292461 = | 16 (0.920) | 5 (0.310) | 5/250 | 1.5 | 24.6% | intergenic (+96/+48) | galU/hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS |
| ? | NC_000913_3_pae_pgi | 1292486 = | 16 (1.000) | intergenic (+121/+23) | galU/hns | glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS | |||||
| * | ? | NC_000913_3_pae_pgi | 1786712 = | 11 (0.630) | 3 (0.180) | 3/264 | 2.2 | 21.7% | coding (401/2379 nt) | ppsA | phosphoenolpyruvate synthase |
| ? | NC_000913_3_pae_pgi | 1786747 = | 11 (0.650) | coding (366/2379 nt) | ppsA | phosphoenolpyruvate synthase | |||||
| * | ? | NC_000913_3_pae_pgi | 2477002 = | 18 (1.040) | 4 (0.250) | 4/248 | 1.7 | 22.6% | coding (628/936 nt) | dsdC | dsd operon activator; autorepressor |
| ? | NC_000913_3_pae_pgi | 2477035 = | 11 (0.700) | coding (595/936 nt) | dsdC | dsd operon activator; autorepressor | |||||
| * | ? | NC_000913_3_pae_pgi | 2568139 = | NA (NA) | 4 (0.240) | 4/258 | 1.8 | NA | noncoding (1/183 nt) | REP178 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP178 (repetitive extragenic palindromic) element; contains 4 REP sequences |
| ? | NC_000913_3_pae_pgi | 2568169 = | NA (NA) | noncoding (31/183 nt) | REP178 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP178 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913_3_pae_pgi | = 2700861 | 15 (0.870) | 5 (0.310) | 4/250 | 1.8 | 25.8% | coding (138/381 nt) | acpS | holo‑[acyl‑carrier‑protein] synthase 1 |
| ? | NC_000913_3_pae_pgi | = 2700868 | 15 (0.940) | coding (131/381 nt) | acpS | holo‑[acyl‑carrier‑protein] synthase 1 | |||||
| * | ? | NC_000913_3_pae_pgi | = 2796251 | 13 (0.750) | 5 (0.310) | 5/254 | 1.5 | 26.9% | coding (578/663 nt) | csiR | transcriptional repressor of csiD |
| ? | NC_000913_3_pae_pgi | = 2796261 | 15 (0.930) | coding (588/663 nt) | csiR | transcriptional repressor of csiD | |||||
| * | ? | NC_000913_3_pae_pgi | = 3943624 | NA (NA) | 5 (0.300) | 5/258 | 1.5 | 56.9% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_pae_pgi | = 4037457 | 4 (0.230) | intergenic (+122/‑62) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||