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 53 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 | 3,946,289 | 0 | T | C | 72.9% | 36.3 / 95.2 | 133 | noncoding (2586/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,264 | 0 | T | A | 72.1% | 73.9 / 169.7 | 185 | noncoding (2561/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,271 | 0 | T | C | 71.8% | 63.1 / 135.4 | 181 | noncoding (2568/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,263 | 0 | A | C | 71.8% | 68.2 / 152.2 | 188 | noncoding (2560/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,352 | 0 | C | T | 71.4% | 4.1 / 11.3 | 21 | noncoding (2649/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,309 | 0 | C | T | 70.8% | 30.1 / 74.0 | 96 | noncoding (2606/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,250 | 0 | A | T | 70.0% | 105.6 / 212.8 | 211 | noncoding (2547/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,251 | 0 | T | G | 70.0% | 96.1 / 188.1 | 210 | noncoding (2548/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,331 | 0 | C | T | 70.0% | 22.4 / 37.5 | 50 | noncoding (2628/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,233 | 0 | A | T | 69.4% | 123.4 / 231.8 | 229 | noncoding (2530/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,241 | 0 | C | T | 69.4% | 100.7 / 182.0 | 219 | noncoding (2538/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,237 | 0 | A | C | 68.6% | 115.0 / 207.2 | 224 | noncoding (2534/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,343 | 0 | G | A | 68.2% | 6.9 / 13.6 | 22 | noncoding (2640/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,344 | 0 | G | A | 68.2% | 7.9 / 14.8 | 22 | noncoding (2641/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,345 | 0 | G | A | 68.2% | 7.9 / 14.9 | 22 | noncoding (2642/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,347 | 0 | G | A | 68.2% | 5.9 / 12.7 | 22 | noncoding (2644/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,180 | 0 | T | C | 67.8% | 84.7 / 138.0 | 152 | noncoding (2477/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,339 | 0 | C | T | 67.7% | 14.7 / 23.5 | 31 | noncoding (2636/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,161 | 0 | G | T | 67.2% | 80.5 / 129.2 | 116 | noncoding (2458/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,219 | 0 | A | G | 67.1% | 116.8 / 199.1 | 211 | noncoding (2516/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 376 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 2700550 = | 115 (1.230) | 14 (0.180) | 14/224 | 7.6 | 12.4% | noncoding (31/77 nt) | ohsC | sRNA antisense regulator of shoB toxin |
| ? | NC_000913_3_hsa_tpiA | 2700601 = | 100 (1.250) | intergenic (+5/+17) | ohsC/acpS | sRNA antisense regulator of shoB toxin/holo‑[acyl‑carrier‑protein] synthase 1 | |||||
| * | ? | NC_000913_3_hsa_tpiA | 2906594 = | 97 (1.040) | 17 (0.200) | 15/236 | 7.7 | 16.6% | intergenic (+11/+49) | ygcG/eno | TPM domain protein, putative phosphatase/enolase |
| ? | NC_000913_3_hsa_tpiA | 2906624 = | 83 (0.990) | intergenic (+41/+19) | ygcG/eno | TPM domain protein, putative phosphatase/enolase | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1570598 = | 112 (1.200) | 15 (0.180) | 15/238 | 7.7 | 13.2% | intergenic (‑109/+47) | gadC/gadB | glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent |
| ? | NC_000913_3_hsa_tpiA | 1570626 = | 96 (1.130) | intergenic (‑137/+19) | gadC/gadB | glutamate:gamma‑aminobutyric acid antiporter/glutamate decarboxylase B, PLP‑dependent | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1285189 | 91 (0.980) | 14 (0.160) | 14/244 | 8.3 | 14.8% | coding (51/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| ? | NC_000913_3_hsa_tpiA | = 1285193 | 76 (0.880) | coding (55/711 nt) | narJ | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 59296 | 95 (1.020) | 13 (0.160) | 12/228 | 8.5 | 13.6% | 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 | 83 (1.020) | 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 | 998439 = | 90 (0.970) | 13 (0.150) | 13/244 | 8.7 | 13.5% | intergenic (+32/‑51) | elfA/elfD | laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone |
| ? | NC_000913_3_hsa_tpiA | 998461 = | 83 (0.960) | intergenic (+54/‑29) | elfA/elfD | laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 2972651 | 112 (1.200) | 12 (0.140) | 12/238 | 8.9 | 10.7% | intergenic (+14/+18) | tas/lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter |
| ? | NC_000913_3_hsa_tpiA | = 2972653 | 99 (1.170) | intergenic (+16/+16) | tas/lplT | putative NADP(H)‑dependent aldo‑keto reductase/lysophospholipid transporter | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3786886 = | 100 (1.070) | 14 (0.160) | 12/242 | 9.1 | 12.7% | coding (49/1260 nt) | envC | activator of AmiB,C murein hydrolases, septal ring factor |
| ? | NC_000913_3_hsa_tpiA | 3786913 = | 100 (1.160) | coding (76/1260 nt) | envC | activator of AmiB,C murein hydrolases, septal ring factor | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 2079003 | 95 (1.020) | 12 (0.140) | 11/234 | 9.2 | 12.7% | intergenic (+72/+29) | yoeF/yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein |
| ? | NC_000913_3_hsa_tpiA | = 2079004 | 80 (0.960) | intergenic (+73/+28) | yoeF/yeeX | pseudogene, CP4‑44 putative prophage remnant;Phage or Prophage Related/UPF0265 family protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 382205 | NA (NA) | 16 (0.170) | 13/260 | 9.3 | NA | coding (532/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913_3_hsa_tpiA | = 382224 | NA (NA) | coding (551/906 nt) | insD1 | IS2 transposase TnpB | |||||