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 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_tpiA | 1,544,021 | 1 | . | A | 73.9% | 56.6 / 17.4 | 23 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| * | NC_000913_3_pae_tpiA | 4,295,976 | 0 | C | T | 25.0% | 84.1 / 30.5 | 59 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913_3_pae_tpiA | 1,544,022 | 1 | . | A | 21.7% | 50.5 / 18.6 | 23 | coding (39/1389 nt) | narU | nitrate/nitrite transporter |
| Marginal new junction evidence (lowest skew 10 of 93 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | = 3488981 | NA (NA) | 6 (0.180) | 6/272 | 3.6 | NA | coding (1200/1221 nt) | argD | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase |
| ? | NC_000913_3_pae_tpiA | = 3488989 | NA (NA) | coding (1192/1221 nt) | argD | bifunctional acetylornithine aminotransferase and succinyldiaminopimelate aminotransferase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228726 | 35 (1.000) | 6 (0.180) | 6/272 | 3.6 | 15.2% | intergenic (+64/‑30) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | 2726206 = | NA (NA) | intergenic (‑18/+75) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3946053 | 3 (0.090) | 8 (0.230) | 6/276 | 3.7 | 73.3% | noncoding (2350/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon |
| ? | NC_000913_3_pae_tpiA | = 3946069 | NA (NA) | noncoding (2366/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228108 | NA (NA) | 7 (0.210) | 6/276 | 3.7 | NA | noncoding (2350/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 228124 | NA (NA) | noncoding (2366/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4291427 | 45 (1.280) | 5 (0.150) | 5/264 | 3.9 | 10.4% | intergenic (+79/‑1) | nrfD/nrfE | formate‑dependent nitrite reductase, membrane subunit/heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| ? | NC_000913_3_pae_tpiA | = 4291429 | 44 (1.350) | coding (2/1659 nt) | nrfE | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4150329 | 63 (1.800) | 5 (0.150) | 5/266 | 3.9 | 7.7% | intergenic (‑148/+34) | eptC/ppc | LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase |
| ? | NC_000913_3_pae_tpiA | = 4150339 | 61 (1.860) | intergenic (‑158/+24) | eptC/ppc | LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 4296196 | 1 (0.030) | 5 (0.150) | 5/270 | 4.0 | 33.4% | noncoding (446/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites |
| ? | NC_000913_3_pae_tpiA | = 4296279 | 19 (0.570) | noncoding (529/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228726 | 35 (1.000) | 5 (0.150) | 5/272 | 4.0 | 13.0% | intergenic (+64/‑30) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 4040499 | NA (NA) | intergenic (+76/‑18) | rrlA/rrfA | 23S ribosomal RNA of rrnA operon/5S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228726 | 35 (1.000) | 5 (0.150) | 5/272 | 4.0 | 14.0% | intergenic (+64/‑30) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 3946682 | 28 (0.830) | intergenic (+75/‑18) | rrlC/rrfC | 23S ribosomal RNA of rrnC operon/5S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 228726 | 35 (1.000) | 5 (0.150) | 5/272 | 4.0 | 13.1% | intergenic (+64/‑30) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | = 228738 | 33 (0.980) | intergenic (+76/‑18) | rrlH/rrfH | 23S ribosomal RNA of rrnH operon/5S ribosomal RNA of rrnH operon | |||||