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 | 4,296,060 | 0 | C | T | 29.6% | 76.9 / 39.1 | 54 | intergenic (+266/+376) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| * | NC_000913 | 125,489 | 0 | G | A | 25.5% | 87.5 / 29.9 | 51 | G825S (GGT→AGT) | aceE | pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding |
| * | NC_000913 | 1,552,257 | 0 | C | A | 23.5% | 75.6 / 10.9 | 34 | intergenic (+266/+141) | fdnI/yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 2,761,620 | 0 | T | G | 20.9% | 84.3 / 24.1 | 43 | K641Q (AAG→CAG) | yfjK | radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage |
| * | NC_000913 | 1,214,511 | 0 | G | C | 20.7% | 64.7 / 13.6 | 29 | P322R (CCT→CGT) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| * | NC_000913 | 1,214,515 | 0 | G | T | 20.7% | 60.1 / 11.6 | 29 | Q321K (CAG→AAG) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| * | NC_000913 | 1,214,516 | 0 | G | C | 20.7% | 65.8 / 13.7 | 29 | F320L (TTC→TTG) ‡ | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| * | NC_000913 | 1,214,517 | 0 | A | C | 20.7% | 55.5 / 12.0 | 29 | F320C (TTC→TGC) ‡ | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| * | NC_000913 | 1,214,521 | 0 | G | C | 20.7% | 63.9 / 13.2 | 29 | R319G (CGC→GGC) | bluF | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| * | NC_000913 | 1,552,256 | 0 | G | A | 20.6% | 71.6 / 12.2 | 34 | intergenic (+265/+142) | fdnI/yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| * | NC_000913 | 2,761,623 | 0 | C | A | 20.4% | 101.3 / 20.5 | 44 | V640L (GTA→TTA) | yfjK | radiation resistance protein; DEAD/H helicase‑like protein; CP4‑57 putative defective prophage |
| * | NC_000913 | 1,322,398 | 0 | C | G | 20.0% | 56.2 / 10.1 | 25 | V183V (GTG→GTC) | trpE | component I of anthranilate synthase |
| * | NC_000913 | 1,757,688 | 0 | T | A | 20.0% | 90.1 / 20.1 | 45 | intergenic (+31/+33) | lpp/ldtE | murein lipoprotein/murein L,D‑transpeptidase |
| * | NC_000913 | 3,183,350 | 0 | A | . | 20.0% | 80.6 / 15.7 | 31 | intergenic (+27/+463) | zupT/ribB | zinc transporter/3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase |
| Marginal new junction evidence (lowest skew 10 of 70 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1207805 | 34 (0.820) | 7 (0.190) | 7/226 | 3.3 | 19.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 30 (0.820) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 227239 = | NA (NA) | 10 (0.240) | 8/254 | 3.3 | NA | noncoding (1481/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | 227267 = | NA (NA) | noncoding (1509/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 6 (0.150) | 6/244 | 3.8 | 32.8% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 4037457 | 13 (0.310) | intergenic (+122/‑62) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | 2738913 = | NA (NA) | 5 (0.130) | 5/234 | 4.0 | NA | intergenic (+8/+35) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| ? | NC_000913 | 2738941 = | NA (NA) | intergenic (+36/+7) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase | |||||
| * | ? | NC_000913 | = 3943624 | NA (NA) | 5 (0.130) | 5/244 | 4.2 | 17.5% | intergenic (+114/‑80) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | NC_000913 | = 3943642 | 25 (0.600) | intergenic (+132/‑62) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon | |||||
| * | ? | NC_000913 | 3910314 = | 32 (0.770) | 5 (0.130) | 5/246 | 4.2 | 13.1% | coding (85/960 nt) | pstC | phosphate ABC transporter permease |
| ? | NC_000913 | 3910344 = | 36 (0.910) | coding (55/960 nt) | pstC | phosphate ABC transporter permease | |||||
| * | ? | NC_000913 | 3175946 = | 64 (1.530) | 6 (0.150) | 5/244 | 4.2 | 9.3% | coding (61/582 nt) | yqiA | acyl CoA esterase |
| ? | NC_000913 | 3175974 = | 56 (1.420) | coding (33/582 nt) | yqiA | acyl CoA esterase | |||||
| * | ? | NC_000913 | 1543030 = | 45 (1.080) | 6 (0.150) | 5/244 | 4.2 | 13.2% | coding (1031/1389 nt) | narU | nitrate/nitrite transporter |
| ? | NC_000913 | 1543053 = | 36 (0.910) | coding (1008/1389 nt) | narU | nitrate/nitrite transporter | |||||
| * | ? | NC_000913 | = 1316079 | 41 (0.980) | 5 (0.130) | 5/242 | 4.2 | 11.2% | intergenic (‑44/+337) | yciG/trpA | KGG family protein/tryptophan synthase, alpha subunit |
| ? | NC_000913 | = 1316088 | 41 (1.050) | intergenic (‑53/+328) | yciG/trpA | KGG family protein/tryptophan synthase, alpha subunit | |||||
| * | ? | NC_000913 | 4534130 = | 47 (1.130) | 4 (0.100) | 4/238 | 4.5 | 9.4% | intergenic (‑77/+300) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment |
| ? | NC_000913 | 4534171 = | 34 (0.880) | intergenic (‑118/+259) | yjhX/yjhZ | UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment | |||||