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 | 2,170,734 | 0 | G | T | 29.7% | 96.1 / 15.8 | 64 | intergenic (‑51/+257) | gatY/fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| * | CP009273 | 838,652 | 0 | T | G | 29.3% | 160.8 / 25.4 | 99 | F289V (TTT→GTT) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 2,632,628 | 0 | C | G | 27.8% | 165.4 / 15.1 | 74 | E5D (GAG→GAC) | yfgM | putative anti‑RcsB factor |
| * | CP009273 | 2,178,908 | 0 | T | G | 26.0% | 136.9 / 26.1 | 77 | intergenic (‑128/+95) | thiM/rcnR | hydoxyethylthiazole kinase/transcriptional repressor of rcnA |
| * | CP009273 | 1,859,025 | 0 | T | C | 25.0% | 136.7 / 51.5 | 81 | intergenic (+34/+14) | yeaD/yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| * | CP009273 | 1,828,727 | 0 | G | C | 24.6% | 126.6 / 17.9 | 66 | E119Q (GAA→CAA) ‡ | ydjY | putative ferrodoxin‑like lipoprotein |
| * | CP009273 | 1,828,729 | 0 | A | C | 23.4% | 121.9 / 14.1 | 64 | E119D (GAA→GAC) ‡ | ydjY | putative ferrodoxin‑like lipoprotein |
| * | CP009273 | 1,859,015 | 0 | G | A | 22.2% | 186.1 / 51.6 | 91 | intergenic (+24/+24) | yeaD/yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| * | CP009273 | 3,997,395 | 0 | G | C | 22.1% | 223.4 / 13.9 | 92 | F48L (TTC→TTG) | rarD | putative chloramphenical resistance permease |
| * | CP009273 | 1,859,020 | 0 | A | T | 21.7% | 184.3 / 48.8 | 93 | intergenic (+29/+19) | yeaD/yeaE | D‑hexose‑6‑phosphate epimerase‑like protein/aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent |
| * | CP009273 | 838,658 | 0 | G | T | 21.3% | 229.4 / 19.0 | 108 | A291S (GCC→TCC) | rlmF | 23S rRNA m(6)A1618 methyltransferase, SAM‑dependent |
| * | CP009273 | 3,448,816 | 0 | T | A | 21.2% | 66.2 / 13.6 | 33 | intergenic (‑59/‑121) | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | CP009273 | 3,448,818 | 0 | A | T | 21.2% | 67.2 / 15.0 | 33 | intergenic (‑61/‑119) | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | CP009273 | 4,402,598 | 0 | C | G | 20.8% | 185.6 / 13.9 | 73 | S132C (TCT→TGT) | yjfM | DUF1190 family protein |
| * | CP009273 | 3,448,820 | 0 | T | A | 20.6% | 69.4 / 13.5 | 34 | intergenic (‑63/‑117) | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| Marginal new junction evidence (lowest skew 10 of 269 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 269749 = | NA (NA) | 38 (0.340) | 25/256 | 5.5 | NA | noncoding (1112/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 269794 = | NA (NA) | noncoding (1067/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 220861 | NA (NA) | 33 (0.300) | 22/254 | 6.1 | NA | noncoding (604/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | CP009273 | = 220890 | NA (NA) | noncoding (633/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 3937006 = | NA (NA) | 32 (0.280) | 20/260 | 6.8 | NA | intergenic (+136/‑58) | gltU/rrlC | tRNA‑Glu/23S ribosomal RNA of rrnC operon |
| ? | CP009273 | 3937076 = | NA (NA) | noncoding (13/2904 nt) | rrlC | 23S ribosomal RNA of rrnC operon | |||||
| * | ? | CP009273 | 2060032 = | 53 (0.450) | 26 (0.230) | 17/254 | 7.4 | 34.1% | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2095685 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 270058 = | NA (NA) | 26 (0.230) | 17/254 | 7.4 | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 270121 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 269672 = | NA (NA) | 20 (0.170) | 18/264 | 7.4 | NA | noncoding (1189/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 269808 = | NA (NA) | noncoding (1053/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 4398990 | 103 (0.990) | 17 (0.160) | 15/238 | 7.6 | 14.2% | noncoding (21/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | CP009273 | = 4399051 | NA (NA) | noncoding (82/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | = 1390859 | NA (NA) | 21 (0.190) | 16/258 | 7.8 | 19.3% | coding (527/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | CP009273 | 1422430 = | 91 (0.770) | noncoding (622/1196 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 1057913 | 136 (1.250) | 21 (0.200) | 15/244 | 7.8 | 13.6% | noncoding (51/134 nt) | REP91 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP91 (repetitive extragenic palindromic) element; contains 3 REP sequences |
| ? | CP009273 | = 1057996 | NA (NA) | noncoding (134/134 nt) | REP91 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP91 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | CP009273 | 270239 = | NA (NA) | 21 (0.190) | 16/258 | 7.8 | NA | noncoding (34/335 nt) | IS911 | repeat region |
| ? | CP009273 | 270302 = | NA (NA) | noncoding (97/335 nt) | IS911 | repeat region | |||||