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 42 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 | 3,946,140 | 0 | G | T | 46.5% | 51.5 / 58.7 | 44 | noncoding (2437/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,180 | 0 | T | C | 46.2% | 101.0 / 106.8 | 78 | noncoding (2477/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,189 | 0 | C | G | 45.8% | 118.0 / 124.0 | 83 | noncoding (2486/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,191 | 0 | G | A | 45.8% | 110.8 / 108.3 | 83 | noncoding (2488/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,192 | 0 | T | G | 45.2% | 107.0 / 127.4 | 84 | noncoding (2489/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,161 | 0 | G | T | 45.0% | 81.8 / 76.4 | 60 | noncoding (2458/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,164 | 0 | A | C | 45.0% | 81.7 / 81.4 | 60 | noncoding (2461/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,165 | 0 | C | T | 44.3% | 84.9 / 66.2 | 61 | noncoding (2462/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,144 | 0 | T | C | 42.5% | 59.7 / 52.8 | 47 | noncoding (2441/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,121 | 0 | A | G | 42.3% | 31.4 / 29.7 | 26 | noncoding (2418/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,167 | 0 | G | C | 42.2% | 98.1 / 89.0 | 64 | noncoding (2464/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,263 | 0 | A | C | 41.7% | 142.2 / 126.8 | 96 | noncoding (2560/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,219 | 0 | A | G | 41.3% | 154.1 / 120.1 | 104 | noncoding (2516/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,945,666 | 0 | T | C | 40.5% | 44.6 / 40.1 | 37 | noncoding (1963/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,233 | 0 | A | T | 39.7% | 183.3 / 153.8 | 117 | noncoding (2530/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,250 | 0 | A | T | 39.1% | 183.3 / 139.8 | 110 | noncoding (2547/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,251 | 0 | T | G | 39.1% | 171.8 / 139.6 | 110 | noncoding (2548/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,237 | 0 | A | C | 38.9% | 176.7 / 143.4 | 113 | noncoding (2534/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,264 | 0 | T | A | 37.9% | 162.6 / 121.6 | 96 | noncoding (2561/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,241 | 0 | C | T | 37.5% | 173.9 / 118.3 | 112 | noncoding (2538/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 113 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | = 1207805 | 35 (0.630) | 14 (0.280) | 12/262 | 4.3 | 29.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | = 1209602 | 35 (0.700) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1207790 = | 36 (0.640) | 11 (0.220) | 11/262 | 4.7 | 24.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 1209619 = | 36 (0.720) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_tpiA | 151509 = | 70 (1.250) | 8 (0.150) | 7/274 | 6.5 | 11.2% | coding (91/597 nt) | yadK | putative fimbrial‑like adhesin protein |
| ? | NC_000913_3_hsa_tpiA | 151533 = | 62 (1.190) | coding (67/597 nt) | yadK | putative fimbrial‑like adhesin protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4542672 | 57 (1.020) | 7 (0.130) | 7/276 | 6.6 | 13.2% | 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 | 39 (0.740) | 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 | = 4114517 | 114 (2.040) | 7 (0.130) | 7/276 | 6.6 | 6.0% | intergenic (‑63/+34) | fpr/glpX | ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II |
| ? | NC_000913_3_hsa_tpiA | = 4114521 | 111 (2.120) | intergenic (‑67/+30) | fpr/glpX | ferredoxin‑NADP reductase; flavodoxin reductase/fructose 1,6‑bisphosphatase II | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3620057 = | NA (NA) | 7 (0.130) | 7/282 | 6.7 | 100% | coding (866/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913_3_hsa_tpiA | 3620067 = | 0 (0.000) | coding (876/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913_3_hsa_tpiA | 730442 = | 24 (0.430) | 7 (0.130) | 7/282 | 6.7 | 23.3% | coding (860/4194 nt) | rhsC | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913_3_hsa_tpiA | 3620073 = | NA (NA) | coding (882/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3705896 = | 78 (1.390) | 6 (0.110) | 6/278 | 7.1 | 7.5% | intergenic (‑106/+202) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor |
| ? | NC_000913_3_hsa_tpiA | 3705924 = | NA (NA) | intergenic (‑134/+174) | dppB/dppA | dipeptide/heme ABC transporter permease/dipeptide/heme ABC transporter periplasmic binding protein; dipeptide chemotaxis receptor | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 381669 | NA (NA) | 6 (0.110) | 6/280 | 7.1 | NA | coding (319/366 nt) | insC1 | IS2 repressor TnpA |
| ? | NC_000913_3_hsa_tpiA | = 381695 | NA (NA) | coding (345/366 nt) coding (22/906 nt) |
insC1 insD1 |
IS2 repressor TnpA IS2 transposase TnpB |
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| * | ? | NC_000913_3_hsa_tpiA | = 3944978 | NA (NA) | 6 (0.110) | 6/282 | 7.2 | 10.6% | noncoding (1275/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_hsa_tpiA | = 4038811 | 53 (0.950) | noncoding (1293/2905 nt) | rrlA | 23S ribosomal RNA of rrnA operon | |||||