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 | 161,068 | 0 | A | C | 36.4% | ‑5.2 / 11.0 | 22 | intergenic (+47/‑149) | hrpB/mrcB | putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase |
| * | CP009273 | 2,178,908 | 0 | T | G | 29.5% | 112.6 / 23.4 | 78 | intergenic (‑128/+95) | thiM/rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
| * | CP009273 | 838,652 | 0 | T | G | 29.1% | 187.7 / 26.3 | 117 | F289V (TTT→GTT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 838,672 | 0 | G | T | 27.9% | 226.5 / 23.5 | 129 | M295I (ATG→ATT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 104,041 | 0 | G | T | 27.9% | 92.9 / 27.8 | 61 | intergenic (+80/‑151) | lpxC/secM | UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation |
| * | CP009273 | 2,170,734 | 0 | G | T | 27.0% | 122.4 / 42.1 | 126 | intergenic (‑51/+257) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 418,995 | 0 | T | G | 26.0% | 131.5 / 10.6 | 77 | L341R (CTG→CGG) | malZ | maltodextrin glucosidase |
| * | CP009273 | 838,675 | 0 | C | A | 23.4% | 238.3 / 24.0 | 124 | N296K (AAC→AAA) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 4,402,596 | 0 | T | G | 21.7% | 152.4 / 11.8 | 69 | V131V (GTT→GTG) | yjfM | DUF1190 family protein |
| * | CP009273 | 2,475,299 | 0 | C | A | 21.6% | 181.6 / 12.2 | 88 | M119I (ATG→ATT) | emrY | putative multidrug efflux system |
| * | CP009273 | 2,998,333 | 0 | T | A | 21.1% | 229.3 / 16.2 | 91 | Q271H (CAA→CAT) | ygeV | putative sigma‑54‑interacting transcriptional activator |
| * | CP009273 | 838,658 | 0 | G | T | 20.0% | 221.4 / 11.6 | 115 | A291S (GCC→TCC) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 1203261 | 68 (0.600) | 25 (0.250) | 16/236 | 3.2 | 29.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 58 (0.580) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 312934 = | 98 (0.860) | 8 (0.070) | 8/268 | 6.2 | 7.5% | intergenic (‑54/‑216) | ykgA/ykgQ | pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein/pseudogene, putative dehydrogenase |
| ? | CP009273 | 1462167 = | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | CP009273 | = 312938 | 93 (0.810) | 11 (0.100) | 7/268 | 6.6 | 10.6% | intergenic (‑58/‑212) | ykgA/ykgQ | pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein/pseudogene, putative dehydrogenase |
| ? | CP009273 | 376716 = | NA (NA) | intergenic (‑1/‑91) | yaiX/insC1 | pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA | |||||
| * | ? | CP009273 | 281564 = | 190 (1.660) | 4 (0.040) | 4/252 | 7.8 | 2.2% | coding (459/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter |
| ? | CP009273 | = 281560 | 181 (1.690) | coding (455/1383 nt) | yagG | CP4‑6 prophage; putative sugar transporter | |||||
| * | ? | CP009273 | 126812 = | 110 (0.960) | 3 (0.030) | 3/250 | 8.4 | 2.9% | coding (936/1854 nt) | yacH | uncharacterized protein |
| ? | CP009273 | = 126808 | 98 (0.920) | coding (940/1854 nt) | yacH | uncharacterized protein | |||||
| * | ? | CP009273 | 3608179 = | 171 (1.500) | 3 (0.030) | 3/262 | 8.6 | 2.1% | coding (1153/1575 nt) | nikA | nickel‑binding, heme‑binding periplasmic protein |
| ? | CP009273 | 4540982 = | 116 (1.040) | coding (132/1344 nt) | gntP | fructuronate transporter | |||||
| * | ? | CP009273 | = 1543776 | 142 (1.240) | 5 (0.040) | 3/262 | 8.6 | 3.4% | coding (2119/3048 nt) | fdnG | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| ? | CP009273 | 1543786 = | 144 (1.290) | coding (2129/3048 nt) | fdnG | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible | |||||
| * | ? | CP009273 | = 2309235 | 113 (0.990) | 3 (0.030) | 3/266 | 8.7 | 2.6% | coding (2269/2673 nt) | rcsD | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| ? | CP009273 | 2309241 = | 112 (0.990) | coding (2275/2673 nt) | rcsD | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC | |||||
| * | ? | CP009273 | 2274542 = | 77 (0.670) | 3 (0.030) | 3/268 | 8.8 | 3.1% | coding (432/1761 nt) | yejH | putative ATP‑dependent DNA or RNA helicase |
| ? | CP009273 | 2308983 = | 111 (0.970) | coding (2017/2673 nt) | rcsD | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC | |||||