mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 51 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 | 3,946,251 | 0 | T | G | 55.6% | 195.6 / 257.6 | 180 | noncoding (2548/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,250 | 0 | A | T | 54.7% | 210.1 / 288.7 | 181 | noncoding (2547/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,180 | 0 | T | C | 54.6% | 152.5 / 190.7 | 141 | noncoding (2477/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,189 | 0 | C | G | 54.5% | 170.3 / 240.5 | 145 | noncoding (2486/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,191 | 0 | G | A | 54.5% | 156.6 / 198.4 | 145 | noncoding (2488/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,264 | 0 | T | A | 53.8% | 184.9 / 251.8 | 158 | noncoding (2561/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,271 | 0 | T | C | 53.7% | 159.5 / 199.7 | 149 | noncoding (2568/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,263 | 0 | A | C | 53.5% | 182.7 / 236.8 | 159 | noncoding (2560/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,289 | 0 | T | C | 53.4% | 125.9 / 157.6 | 116 | noncoding (2586/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,237 | 0 | A | C | 53.4% | 219.6 / 280.7 | 190 | noncoding (2534/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,233 | 0 | A | T | 53.4% | 232.3 / 315.4 | 191 | noncoding (2530/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,192 | 0 | T | G | 53.4% | 166.2 / 212.3 | 148 | noncoding (2489/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,219 | 0 | A | G | 53.3% | 201.8 / 248.0 | 180 | noncoding (2516/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,241 | 0 | C | T | 53.2% | 208.4 / 255.3 | 186 | noncoding (2538/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,309 | 0 | C | T | 52.8% | 72.9 / 95.2 | 72 | noncoding (2606/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,161 | 0 | G | T | 51.3% | 148.0 / 201.4 | 113 | noncoding (2458/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,164 | 0 | A | C | 51.3% | 138.3 / 172.8 | 113 | noncoding (2461/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,165 | 0 | C | T | 50.9% | 137.3 / 162.5 | 114 | noncoding (2462/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,167 | 0 | G | C | 50.9% | 151.5 / 207.5 | 114 | noncoding (2464/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,331 | 0 | C | T | 47.8% | 55.5 / 64.1 | 46 | noncoding (2628/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 176 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 4542664 = | 96 (1.060) | 17 (0.200) | 15/262 | 8.0 | 15.2% | 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 = | 100 (1.180) | 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 | = 4201780 | 83 (0.920) | 10 (0.130) | 9/246 | 10.1 | 11.6% | intergenic (‑110/‑128) | zraP/zraS | Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR |
| ? | NC_000913_3_hsa_tpiA | = 4201792 | 79 (0.990) | intergenic (‑122/‑116) | zraP/zraS | Zn‑dependent periplasmic chaperone/sensory histidine kinase in two‑component regulatory system with ZraR | |||||
| * | ? | NC_000913_3_hsa_tpiA | 2727891 = | NA (NA) | 10 (0.120) | 10/268 | 10.3 | NA | noncoding (1294/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_hsa_tpiA | 2727910 = | NA (NA) | noncoding (1275/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3648358 | 85 (0.940) | 9 (0.110) | 9/258 | 10.5 | 9.7% | noncoding (65/84 nt) | agrB | antisense sRNA antitoxin for the DinQ toxin |
| ? | NC_000913_3_hsa_tpiA | = 3648363 | 89 (1.070) | noncoding (70/84 nt) | agrB | antisense sRNA antitoxin for the DinQ toxin | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 256448 | 101 (1.110) | 9 (0.100) | 9/266 | 10.8 | 8.5% | intergenic (+13/‑79) | gpt/frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity |
| ? | NC_000913_3_hsa_tpiA | = 256459 | 98 (1.140) | intergenic (+24/‑68) | gpt/frsA | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase/fermentation‑respiration switch protein; PTS Enzyme IIA(Glc)‑binding protein; pNP‑butyrate esterase activity | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3895233 | 81 (0.890) | 9 (0.110) | 8/256 | 11.0 | 11.0% | intergenic (+15/+39) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter |
| ? | NC_000913_3_hsa_tpiA | = 3895244 | 71 (0.860) | intergenic (+26/+28) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3895222 = | 80 (0.880) | 8 (0.100) | 8/256 | 11.0 | 10.0% | intergenic (+4/+50) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter |
| ? | NC_000913_3_hsa_tpiA | 3895257 = | 71 (0.860) | intergenic (+39/+15) | chrR/adeP | chromate reductase, Class I, flavoprotein/adenine permease, high affinity; adenine:H+ symporter | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1911650 = | 110 (1.210) | 9 (0.110) | 8/256 | 11.0 | 8.2% | intergenic (+1/+45) | yebQ/htpX | putative transporter/putative endopeptidase |
| ? | NC_000913_3_hsa_tpiA | 1911680 = | 100 (1.210) | intergenic (+31/+15) | yebQ/htpX | putative transporter/putative endopeptidase | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1330387 = | 90 (0.990) | 8 (0.100) | 8/260 | 11.1 | 8.7% | intergenic (+6/+30) | sohB/yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN |
| ? | NC_000913_3_hsa_tpiA | 1330413 = | 84 (1.000) | intergenic (+32/+4) | sohB/yciN | inner membrane protein, S49 peptidase family protein/DUF2498 protein YciN | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1097426 = | NA (NA) | 11 (0.120) | 9/276 | 11.1 | 30.9% | intergenic (+597/+139) | ycdU/serX | putative inner membrane protein/tRNA‑Ser |
| ? | NC_000913_3_hsa_tpiA | 1097455 = | 25 (0.280) | intergenic (+626/+110) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||