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 (highest frequency 20 of 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_hsa_tpiA | 3,946,121 | 0 | A | G | 36.2% | 112.5 / 64.7 | 69 | noncoding (2418/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,101 | 0 | T | C | 35.7% | 38.6 / 22.9 | 28 | noncoding (2398/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,180 | 0 | T | C | 34.6% | 379.3 / 196.8 | 205 | noncoding (2477/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,105 | 0 | T | C | 34.4% | 46.1 / 24.6 | 32 | noncoding (2402/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,140 | 0 | G | T | 34.2% | 214.9 / 112.8 | 114 | noncoding (2437/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,161 | 0 | G | T | 34.0% | 309.9 / 161.2 | 159 | noncoding (2458/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,144 | 0 | T | C | 33.3% | 211.3 / 103.2 | 117 | noncoding (2441/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,219 | 0 | A | G | 33.2% | 544.2 / 263.3 | 285 | noncoding (2516/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,164 | 0 | A | C | 32.9% | 315.3 / 184.0 | 165 | noncoding (2461/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,165 | 0 | C | T | 32.7% | 312.1 / 146.9 | 165 | noncoding (2462/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,251 | 0 | T | G | 32.4% | 606.9 / inf | 298 | noncoding (2548/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,264 | 0 | T | A | 32.4% | 547.9 / 266.1 | 261 | noncoding (2561/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,271 | 0 | T | C | 32.1% | 490.7 / 222.6 | 249 | noncoding (2568/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,250 | 0 | A | T | 32.0% | 635.4 / inf | 300 | noncoding (2547/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,191 | 0 | G | A | 32.0% | 433.6 / 189.4 | 220 | noncoding (2488/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,189 | 0 | C | G | 31.8% | 465.7 / 244.4 | 220 | noncoding (2486/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,167 | 0 | G | C | 31.6% | 362.1 / 187.8 | 171 | noncoding (2464/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,263 | 0 | A | C | 31.5% | 551.9 / 286.6 | 267 | noncoding (2560/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,241 | 0 | C | T | 31.4% | 612.4 / 269.3 | 307 | noncoding (2538/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,237 | 0 | A | C | 30.8% | 655.5 / inf | 315 | noncoding (2534/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 141 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 154 (0.690) | 45 (0.230) | 36/246 | 12.3 | 23.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 158 (0.800) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 136 (0.610) | 40 (0.200) | 32/246 | 13.7 | 22.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 153 (0.780) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4542672 | 174 (0.780) | 40 (0.190) | 33/260 | 14.3 | 18.3% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_hsa_tpiA | = 4542968 | 195 (0.940) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_hsa_tpiA | 4542664 = | 176 (0.790) | 34 (0.160) | 31/260 | 15.0 | 15.9% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913_3_hsa_tpiA | 4542978 = | 195 (0.940) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_hsa_tpiA | 59280 = | 184 (0.830) | 25 (0.130) | 22/244 | 17.7 | 13.3% | intergenic (+1/+407) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| ? | NC_000913_3_hsa_tpiA | 59320 = | 165 (0.850) | intergenic (+41/+367) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 59296 | 197 (0.890) | 24 (0.120) | 19/244 | 19.1 | 12.4% | intergenic (+17/+391) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent |
| ? | NC_000913_3_hsa_tpiA | = 59302 | 167 (0.860) | intergenic (+23/+385) | yabP/rluA | pseudogene, pentapeptide repeats‑containing/dual specificity 23S rRNA pseudouridine(746), tRNA pseudouridine(32) synthase, SAM‑dependent | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3423376 = | 206 (0.930) | 36 (0.160) | 22/274 | 19.7 | 14.4% | intergenic (+182/+47) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_hsa_tpiA | = 4213144 | 225 (1.030) | intergenic (+3/‑72) | rrfE/yjaA | 5S ribosomal RNA of rrnE operon/stress‑induced protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3648127 | 198 (0.890) | 23 (0.110) | 17/256 | 21.1 | 11.3% | noncoding (65/84 nt) | agrA | inactive antisense sRNA |
| ? | NC_000913_3_hsa_tpiA | = 3648132 | 179 (0.870) | noncoding (70/84 nt) | agrA | inactive antisense sRNA | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3423376 = | 206 (0.930) | 26 (0.120) | 19/274 | 21.2 | 11.3% | intergenic (+182/+47) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_hsa_tpiA | 3423665 = | NA (NA) | intergenic (‑10/+3) | thrV/rrfD | tRNA‑Thr/5S ribosomal RNA of rrnD operon | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3423376 = | 206 (0.930) | 25 (0.110) | 18/274 | 21.7 | 16.4% | intergenic (+182/+47) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913_3_hsa_tpiA | = 3946822 | 52 (0.240) | intergenic (+3/‑50) | rrfC/aspT | 5S ribosomal RNA of rrnC operon/tRNA‑Asp | |||||