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 | ||
| * | CP009273 | 1,995,399 | 0 | A | C | 34.4% | 263.8 / 30.8 | 119 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| * | CP009273 | 3,029,116 | 0 | A | C | 23.9% | 322.3 / 10.3 | 118 | G175G (GGT→GGG) | prfB | peptide chain release factor RF‑2 |
| * | CP009273 | 2,617,862 | 0 | T | G | 23.7% | 361.4 / 21.5 | 132 | V487G (GTA→GGA) | ppk | polyphosphate kinase, component of RNA degradosome |
| * | CP009273 | 4,526,007 | 0 | T | G | 23.0% | 507.0 / 22.1 | 175 | intergenic (+159/+424) | yjhR/nanS | pseudogene, helicase family; putative frameshift suppressor/9‑O‑acetyl N‑acetylneuraminic acid esterase |
| * | CP009273 | 1,508,252 | 0 | A | G | 22.6% | 290.1 / 39.5 | 133 | G55G (GGA→GGG) | ydcU | putative spermidine/putrescine transporter subunit |
| * | CP009273 | 1,267,278 | 0 | T | G | 22.4% | 422.3 / 15.2 | 143 | T10P (ACC→CCC) | chaA | calcium/sodium:proton antiporter |
| * | CP009273 | 3,436,636 | 0 | A | C | 20.8% | 319.2 / 19.4 | 106 | V274G (GTA→GGA) | secY | preprotein translocase membrane subunit |
| * | CP009273 | 4,086,494 | 0 | T | G | 20.4% | 365.8 / 18.7 | 133 | Y102S (TAC→TCC) | rhaM | L‑rhamnose mutarotase |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 3416618 = | 120 (0.720) | 55 (0.040) +GAATTAATTCCCC |
42/174 | 6.4 | 34.5% | intergenic (+65/+164) | yhdZ/rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| ? | KX077536 | 8127 = | NA (NA) | intergenic (+52/–) | unknown/– | cat/– | |||||
| * | ? | CP009273 | 3416618 = | 120 (0.720) | 58 (0.390) +GAATTAATTCC |
43/178 | 6.5 | 33.9% | intergenic (+65/+164) | yhdZ/rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| ? | CP009273 | 4033989 = | 134 (0.810) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 60 (0.390) +AATTCC |
44/188 | 6.9 | 32.3% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | 4033989 = | 134 (0.810) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 360104 = | 135 (0.820) | 56 (0.040) +AATTCCCC |
42/184 | 7.1 | 31.1% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | KX077536 | 8127 = | NA (NA) | intergenic (+52/–) | unknown/– | cat/– | |||||
| * | ? | CP009273 | = 1203261 | 117 (0.710) | 33 (0.240) | 31/168 | 8.9 | 23.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 115 (0.830) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1203246 = | 131 (0.790) | 16 (0.120) | 16/168 | 14.6 | 12.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 119 (0.860) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 4532499 = | 228 (1.380) | 8 (0.050) | 8/182 | 20.3 | 3.7% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 205 (1.360) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 1205074 | 140 (0.850) | 6 (0.040) | 5/170 | 21.7 | 4.1% | pseudogene (2/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
| ? | CP009273 | 2465376 = | 161 (1.150) | pseudogene (226/579 nt) | yfdL | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 77220 | 148 (0.890) | 3 (0.020) | 3/186 | 24.7 | 2.2% | coding (132/1401 nt) | leuC | 3‑isopropylmalate dehydratase large subunit |
| ? | CP009273 | = 749500 | 129 (0.840) | coding (425/1284 nt) | gltA | citrate synthase | |||||