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_pgi | 4,037,227 | 1 | . | T | 26.7% | 7.8 / 14.9 | 15 | intergenic (+10/‑33) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913_3_pae_pgi | 526,792 | 0 | A | C | 25.8% | 460.5 / 206.5 | 261 | S1178R (AGC→CGC) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,796 | 0 | C | G | 25.4% | 595.2 / 208.9 | 257 | A1179G (GCG→GGG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 526,800 | 0 | A | G | 24.3% | 500.4 / 143.1 | 243 | E1180E (GAA→GAG) | rhsD | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| * | NC_000913_3_pae_pgi | 4,037,225 | 0 | A | . | 23.5% | 32.5 / 10.6 | 17 | intergenic (+8/‑35) | ileT/alaT | tRNA‑Ile/tRNA‑Ala |
| * | NC_000913_3_pae_pgi | 4,295,320 | 0 | C | T | 23.3% | 510.9 / 143.5 | 258 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_pgi | 3,439,588 | 0 | G | C | 23.1% | 497.6 / 167.0 | 223 | intergenic (‑79/+28) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913_3_pae_pgi | 3,439,589 | 0 | G | C | 22.1% | 526.5 / 171.0 | 231 | intergenic (‑80/+27) | yhdN/rplQ | DUF1992 family protein/50S ribosomal subunit protein L17 |
| * | NC_000913_3_pae_pgi | 1,015,912 | 0 | T | A | 20.0% | 501.6 / 130.8 | 205 | intergenic (+30/+40) | rmf/fabA | ribosome modulation factor/beta‑hydroxydecanoyl thioester dehydrase |
| Marginal new junction evidence (lowest skew 10 of 1113 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_pgi | = 4541950 | 171 (0.860) | 62 (0.340) | 54/240 | 7.0 | 28.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_pae_pgi | = 4542246 | 150 (0.810) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_pae_pgi | 4541942 = | 164 (0.830) | 47 (0.250) | 42/240 | 10.0 | 23.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_pae_pgi | 4542256 = | 156 (0.840) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_pae_pgi | = 1207805 | 159 (0.800) | 35 (0.200) | 32/226 | 12.2 | 20.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | = 1209602 | 130 (0.750) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 1207790 = | 168 (0.850) | 38 (0.220) | 32/226 | 12.2 | 21.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_pgi | 1209619 = | 133 (0.760) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_pgi | 3423823 = | NA (NA) | 70 (0.370) | 33/246 | 13.2 | 28.4% | intergenic (‑36/+57) | rrfD/rrlD | 5S ribosomal RNA of rrnD operon/23S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_pae_pgi | = 3946688 | 185 (0.930) | intergenic (+81/‑12) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_pgi | = 228744 | 96 (0.480) | 69 (0.360) | 32/246 | 13.6 | 43.0% | intergenic (+82/‑12) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_pgi | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | 2726200 = | NA (NA) | 68 (0.360) | 31/246 | 14.0 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_pgi | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_pgi | = 228108 | NA (NA) | 46 (0.240) | 28/250 | 15.4 | 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 | 1552101 = | NA (NA) | 28 (0.160) | 25/234 | 15.5 | NA | noncoding (31/97 nt) | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_pae_pgi | 1552249 = | NA (NA) | noncoding (1/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_pae_pgi | = 3946053 | 8 (0.040) | 45 (0.230) | 27/250 | 15.8 | 85.3% | noncoding (2350/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_pae_pgi | = 3946069 | NA (NA) | noncoding (2366/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon | |||||