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 | 71,561 | 0 | T | G | 25.9% | 315.5 / 15.9 | 116 | N136T (AAC→ACC) | thiB | thiamine‑, thiamine pyrophosphate‑, thiamine monophosphate‑binding ABC transporter periplasmic protein; ThiBPQ thiamine, thiamine pyrophosphate importer |
| * | CP009273 | 4,151,082 | 0 | A | C | 25.0% | 293.5 / 12.0 | 112 | T11P (ACC→CCC) | fabR | transcriptional repressor of fabA and fabB |
| * | CP009273 | 2,240,108 | 0 | T | G | 23.0% | 319.3 / 10.8 | 114 | A47A (GCA→GCC) | cirA | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| * | CP009273 | 1,995,399 | 0 | A | C | 21.0% | 351.0 / 15.4 | 119 | intergenic (‑129/+192) | fliA/fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin) |
| * | CP009273 | 1,267,278 | 0 | T | G | 20.7% | 372.8 / 19.1 | 121 | T10P (ACC→CCC) | chaA | calcium/sodium:proton antiporter |
| Marginal new junction evidence (lowest skew 10 of 20 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 2282398 = | NA (NA) | 253 (1.850) | 33/200 | 8.7 | 64.4% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 3724821 | 140 (1.020) | coding (331/993 nt) | xylF | D‑xylose transporter subunit | |||||
| * | ? | CP009273 | = 4532507 | 140 (1.020) | 31 (0.250) | 26/182 | 9.7 | 19.6% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | = 4532803 | 127 (1.020) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | 3416618 = | 102 (0.740) | 43 (0.350) +GAATTAATTCC |
25/178 | 9.7 | 28.1% | intergenic (+65/+164) | yhdZ/rrfF | putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon |
| ? | CP009273 | 4033989 = | 145 (1.060) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | 360104 = | NA (NA) | 49 (0.380) +AATTCC |
27/188 | 9.8 | 26.5% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | 4033989 = | 145 (1.060) | noncoding (113/120 nt) | rrfA | 5S ribosomal RNA of rrnA operon | |||||
| * | ? | CP009273 | = 1203261 | 115 (0.840) | 19 (0.170) | 19/168 | 11.3 | 16.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 92 (0.800) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 2283592 | NA (NA) | 71 (0.520) | 21/200 | 12.8 | 32.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3724818 = | 147 (1.070) | coding (328/993 nt) | xylF | D‑xylose transporter subunit | |||||
| * | ? | CP009273 | 4532499 = | 151 (1.100) | 17 (0.140) | 16/182 | 13.7 | 11.4% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | CP009273 | 4532813 = | 128 (1.030) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||
| * | ? | CP009273 | = 2060834 | NA (NA) | 19 (0.140) | 17/200 | 14.5 | 11.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 3724818 = | 147 (1.070) | coding (328/993 nt) | xylF | D‑xylose transporter subunit | |||||
| * | ? | CP009273 | = 4161777 | 0 (0.000) | 3 (0.000) | 3/124 | 17.5 | 100% | intergenic (+93/‑208) | rrfB/murB | 5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding |
| ? | KX077536 | 39 = | 0 (0.000) | intergenic (–/‑1060) | –/unknown | –/BLA | |||||
| * | ? | CP009273 | = 4034089 | 43 (0.310) | 3 (0.000) | 3/124 | 17.5 | 18.5% | intergenic (+93/+177) | rrfA/mobB | 5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B |
| ? | KX077536 | 39 = | 0 (0.000) | intergenic (–/‑1060) | –/unknown | –/BLA | |||||