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 |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_tpiA | 1,544,021 | 1 | . | A | 74.1% | 67.3 / 21.2 | 28 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| * | NC_000913_3_pae_tpiA | 4,295,976 | 0 | C | T | 21.1% | 96.5 / 19.4 | 58 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Marginal new junction evidence (lowest skew 10 of 304 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 3423823 = | NA (NA) | 11 (0.280) | 7/274 | 4.2 | 100% | intergenic (‑36/+57) | rrfD/rrlD | 5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_pae_tpiA | = 3946688 | 0 (0.000) | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 3423817 = | 0 (0.000) | 11 (0.280) | 7/274 | 4.2 | 100% | intergenic (‑30/+63) | rrfD/rrlD | 5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_pae_tpiA | = 4040499 | NA (NA) | intergenic (+76/‑18) | rrlA/rrfA | 23S ribosomal RNA of rrnA operon/5S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 2726200 = | NA (NA) | 10 (0.250) | 7/274 | 4.2 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_tpiA | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228744 | 35 (0.850) | 10 (0.250) | 7/274 | 4.2 | 23.0% | intergenic (+82/‑12) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 3708415 = | 36 (0.870) | 6 (0.160) | 6/262 | 4.4 | 16.2% | intergenic (‑710/+201) | dppA/proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro |
| ? | NC_000913_3_pae_tpiA | 3708442 = | 29 (0.770) | intergenic (‑737/+174) | dppA/proK | dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor/tRNA‑Pro | |||||
| * | ? | NC_000913_3_pae_tpiA | 1954429 = | NA (NA) | 6 (0.150) | 6/272 | 4.6 | 10.9% | noncoding (1/98 nt) | RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP139 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_tpiA | 2236680 = | 49 (1.250) | noncoding (147/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4542606 | 43 (1.040) | 5 (0.130) | 5/268 | 5.0 | 10.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_pae_tpiA | = 4542902 | 47 (1.210) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_pae_tpiA | 2549484 = | NA (NA) | 5 (0.130) | 5/272 | 5.0 | NA | noncoding (19/98 nt) | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP176 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_tpiA | 3676128 = | NA (NA) | noncoding (8/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_tpiA | 2236680 = | 49 (1.250) | 5 (0.130) | 5/272 | 5.0 | 9.3% | noncoding (147/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_pae_tpiA | 3639209 = | NA (NA) | noncoding (1/98 nt) | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP261 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_tpiA | 2236680 = | 49 (1.250) | 5 (0.130) | 5/272 | 5.0 | 9.3% | noncoding (147/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | NC_000913_3_pae_tpiA | = 2945992 | NA (NA) | noncoding (97/97 nt) | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP206 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||