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 33 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 | 1,544,021 | 1 | . | A | 72.4% | 74.1 / 26.3 | 29 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| * | NC_000913_3_hsa_tpiA | 264,098 | 0 | G | T | 71.9% | 38.8 / 26.3 | 32 | L50L (CTC→CTA) | ykfH | uncharacterized protein |
| * | NC_000913_3_hsa_tpiA | 482,230 | 0 | G | A | 70.0% | 74.6 / 28.9 | 51 | P725L (CCG→CTG) | acrB | multidrug efflux system protein |
| * | NC_000913_3_hsa_tpiA | 2,817,170 | 0 | C | A | 67.3% | 51.5 / 47.8 | 52 | E112* (GAA→TAA) | yqaB | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| * | NC_000913_3_hsa_tpiA | 3,946,237 | 0 | A | C | 36.8% | 90.2 / 73.5 | 58 | noncoding (2534/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,241 | 0 | C | T | 36.8% | 88.0 / 54.7 | 57 | noncoding (2538/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,250 | 0 | A | T | 36.8% | 92.2 / 68.4 | 57 | noncoding (2547/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,251 | 0 | T | G | 36.8% | 90.1 / 68.0 | 57 | noncoding (2548/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,233 | 0 | A | T | 36.1% | 104.5 / 72.2 | 61 | noncoding (2530/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,192 | 0 | T | G | 34.6% | 82.9 / 53.1 | 52 | noncoding (2489/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 1,529,218 | 0 | C | T | 34.4% | 38.3 / 26.4 | 32 | pseudogene (1317/2037 nt) | rhsE | pseudogene, Rhs family |
| * | NC_000913_3_hsa_tpiA | 3,946,140 | 0 | G | T | 34.4% | 57.8 / 21.7 | 32 | noncoding (2437/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,161 | 0 | G | T | 34.2% | 73.4 / 33.2 | 41 | noncoding (2458/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,180 | 0 | T | C | 34.0% | 75.8 / 41.7 | 47 | noncoding (2477/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,189 | 0 | C | G | 34.0% | 88.6 / 56.2 | 50 | noncoding (2486/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,191 | 0 | G | A | 34.0% | 85.3 / 38.0 | 50 | noncoding (2488/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 4,296,042 | 0 | C | T | 33.8% | 70.7 / 58.0 | 71 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_hsa_tpiA | 3,946,121 | 0 | A | G | 33.3% | 35.9 / 14.8 | 21 | noncoding (2418/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,164 | 0 | A | C | 33.3% | 71.2 / 41.7 | 42 | noncoding (2461/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| * | NC_000913_3_hsa_tpiA | 3,946,165 | 0 | C | T | 33.3% | 72.5 / 34.2 | 42 | noncoding (2462/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | 15391 = | NA (NA) | 11 (0.210) | 10/288 | 5.2 | 28.1% | intergenic (+93/‑54) | dnaJ/insL1 | chaperone Hsp40, DnaK co‑chaperone/IS186 transposase |
| ? | NC_000913_3_hsa_tpiA | = 458799 | 29 (0.550) | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3652634 = | NA (NA) | 4 (0.090) +28 bp |
4/240 | 6.9 | NA | coding (565/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913_3_hsa_tpiA | = 4110740 | NA (NA) | intergenic (+55/+857) | cdh/yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3304806 = | 65 (1.230) | 6 (0.120) | 6/286 | 6.9 | 8.8% | coding (1012/1245 nt) | mtr | tryptophan transporter of high affinity |
| ? | NC_000913_3_hsa_tpiA | 3304828 = | 61 (1.190) | coding (990/1245 nt) | mtr | tryptophan transporter of high affinity | |||||
| * | ? | NC_000913_3_hsa_tpiA | 1428198 = | 53 (1.000) | 4 (0.090) +28 bp |
4/240 | 6.9 | 8.5% | coding (529/981 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913_3_hsa_tpiA | = 4110740 | NA (NA) | intergenic (+55/+857) | cdh/yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | 2349900 = | 36 (0.680) | 6 (0.110) | 6/296 | 7.1 | 14.8% | intergenic (+7/+35) | yfaH/glpQ | pseudogene/periplasmic glycerophosphodiester phosphodiesterase |
| ? | NC_000913_3_hsa_tpiA | 2349928 = | 33 (0.620) | intergenic (+35/+7) | yfaH/glpQ | pseudogene/periplasmic glycerophosphodiester phosphodiesterase | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3042313 | 72 (1.360) | 6 (0.120) | 5/274 | 7.2 | 8.2% | intergenic (+20/+176) | ygfZ/yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein |
| ? | NC_000913_3_hsa_tpiA | = 3042320 | 68 (1.390) | intergenic (+27/+169) | ygfZ/yqfA | iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 4589090 | 63 (1.190) | 5 (0.100) | 5/280 | 7.3 | 7.7% | intergenic (‑29/+21) | yjiX/yjiY | DUF466 family protein/putative transporter |
| ? | NC_000913_3_hsa_tpiA | = 4589094 | 61 (1.220) | intergenic (‑33/+17) | yjiX/yjiY | DUF466 family protein/putative transporter | |||||
| * | ? | NC_000913_3_hsa_tpiA | 3086111 = | 59 (1.110) | 5 (0.100) | 5/282 | 7.3 | 8.1% | intergenic (‑60/‑76) | yqgB/yqgC | uncharacterized protein/uncharacterized protein |
| ? | NC_000913_3_hsa_tpiA | 3086129 = | 57 (1.130) | intergenic (‑78/‑58) | yqgB/yqgC | uncharacterized protein/uncharacterized protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3012405 | 57 (1.080) | 5 (0.100) | 5/284 | 7.4 | 8.5% | noncoding (5/204 nt) | RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site |
| ? | NC_000913_3_hsa_tpiA | = 3012419 | 53 (1.040) | noncoding (19/204 nt) | RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | RIP209 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 3943643 | NA (NA) | 5 (0.090) | 5/296 | 7.6 | 8.6% | intergenic (+133/‑61) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_hsa_tpiA | = 4037438 | 53 (1.000) | intergenic (+103/‑81) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||