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 | 1,446,357 | 1 | . | T | 26.5% | 58.1 / 41.3 | 34 | intergenic (+151/+21) | ydbL/feaR | DUF1318 family protein/transcriptional activator for tynA and feaB |
| * | NC_000913 | 1,446,362 | 0 | A | . | 26.5% | 84.3 / 27.6 | 34 | intergenic (+156/+16) | ydbL/feaR | DUF1318 family protein/transcriptional activator for tynA and feaB |
| * | NC_000913 | 2,666,978 | 0 | A | G | 25.0% | 36.0 / 10.8 | 24 | L290S (TTG→TCG) ‡ | hcaT | putative 3‑phenylpropionic transporter |
| * | NC_000913 | 2,666,979 | 0 | A | T | 25.0% | 37.0 / 12.4 | 24 | L290M (TTG→ATG) ‡ | hcaT | putative 3‑phenylpropionic transporter |
| * | NC_000913 | 2,666,986 | 0 | A | G | 25.0% | 36.0 / 11.1 | 24 | T287T (ACT→ACC) | hcaT | putative 3‑phenylpropionic transporter |
| * | NC_000913 | 2,666,980 | 0 | C | T | 24.0% | 42.0 / 10.7 | 25 | A289A (GCG→GCA) | hcaT | putative 3‑phenylpropionic transporter |
| * | NC_000913 | 1,388,285 | 0 | A | G | 21.9% | 57.3 / 13.1 | 33 | intergenic (+24/+20) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| * | NC_000913 | 3,831,761 | 0 | C | G | 21.4% | 62.0 / 14.0 | 28 | A435A (GCC→GCG) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| * | NC_000913 | 3,831,764 | 0 | C | G | 21.4% | 63.6 / 13.8 | 28 | A436A (GCC→GCG) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| * | NC_000913 | 2,024,609 | 0 | T | G | 20.8% | 43.1 / 11.0 | 24 | intergenic (+18/+26) | rcsA/dsrB | transcriptional regulator of colanic acid capsular biosynthesis/uncharacterized protein |
| * | NC_000913 | 3,756,563 | 0 | A | G | 20.7% | 52.1 / 10.5 | 29 | intergenic (‑52/+113) | aldB/yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| * | NC_000913 | 3,756,564 | 0 | T | A | 20.7% | 55.1 / 11.7 | 29 | intergenic (‑53/+112) | aldB/yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| * | NC_000913 | 3,756,565 | 0 | C | T | 20.7% | 57.1 / 10.2 | 29 | intergenic (‑54/+111) | aldB/yiaY | aldehyde dehydrogenase B/L‑threonine dehydrogenase |
| * | NC_000913 | 3,831,757 | 0 | C | T | 20.7% | 56.5 / 10.2 | 29 | A434V (GCC→GTC) | yicH | putative inner membrane‑anchored periplasmic AsmA family protein |
| * | NC_000913 | 1,388,284 | 0 | A | T | 20.6% | 74.3 / 10.3 | 34 | intergenic (+23/+21) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| * | NC_000913 | 1,388,283 | 0 | C | T | 20.0% | 73.5 / 10.8 | 36 | intergenic (+22/+22) | tyrR/tpx | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase/lipid hydroperoxide peroxidase |
| Marginal new junction evidence (lowest skew 10 of 29 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4420746 | 34 (0.950) | 6 (0.180) | 6/234 | 3.4 | 16.7% | coding (767/1398 nt) | ulaA | L‑ascorbate‑specific enzyme IIC permease component of PTS |
| ? | NC_000913 | = 4420774 | 28 (0.830) | coding (795/1398 nt) | ulaA | L‑ascorbate‑specific enzyme IIC permease component of PTS | |||||
| * | ? | NC_000913 | 1562837 = | 29 (0.810) | 6 (0.180) | 6/232 | 3.4 | 18.7% | coding (240/582 nt) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent |
| ? | NC_000913 | 1562864 = | 25 (0.750) | coding (213/582 nt) | ddpX | D‑ala‑D‑ala dipeptidase, Zn‑dependent | |||||
| * | ? | NC_000913 | 2940113 = | 30 (0.840) | 7 (0.210) | 5/234 | 3.7 | 19.6% | intergenic (+14/+30) | fucR/rlmM | l‑fucose operon activator/23S rRNA C2498 2'‑O‑ribose methyltransferase, SAM‑dependent |
| ? | NC_000913 | 2940137 = | 29 (0.860) | intergenic (+38/+6) | fucR/rlmM | l‑fucose operon activator/23S rRNA C2498 2'‑O‑ribose methyltransferase, SAM‑dependent | |||||
| * | ? | NC_000913 | = 225084 | NA (NA) | 5 (0.150) | 5/234 | 3.7 | NA | noncoding (1314/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 225092 | NA (NA) | noncoding (1322/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913 | = 2300551 | 38 (1.060) | 5 (0.140) | 5/240 | 3.8 | 11.3% | coding (2203/2487 nt) | napA | nitrate reductase, periplasmic, large subunit |
| ? | NC_000913 | = 2300578 | 42 (1.210) | coding (2176/2487 nt) | napA | nitrate reductase, periplasmic, large subunit | |||||
| * | ? | NC_000913 | 2987089 = | 55 (1.540) | 4 (0.130) | 4/220 | 3.9 | 8.3% | intergenic (+13/‑447) | yqeG/yqeH | putative transporter/putative LuxR family transcriptional regulator |
| ? | NC_000913 | 2987120 = | 40 (1.260) | intergenic (+44/‑416) | yqeG/yqeH | putative transporter/putative LuxR family transcriptional regulator | |||||
| * | ? | NC_000913 | 4240741 = | 39 (1.090) | 4 (0.120) | 4/228 | 4.1 | 9.9% | intergenic (+6/+38) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter |
| ? | NC_000913 | 4240769 = | 37 (1.120) | intergenic (+34/+10) | psiE/xylE | phosphate starvation inducible protein/D‑xylose transporter | |||||
| * | ? | NC_000913 | 3866983 = | 26 (0.730) | 4 (0.120) | 4/234 | 4.1 | 13.0% | intergenic (‑86/+26) | ibpB/ibpA | heat shock chaperone/heat shock chaperone |
| ? | NC_000913 | 3867002 = | 29 (0.860) | intergenic (‑105/+7) | ibpB/ibpA | heat shock chaperone/heat shock chaperone | |||||
| * | ? | NC_000913 | 3423318 = | 41 (1.140) | 4 (0.120) | 4/230 | 4.1 | 9.9% | intergenic (+124/+105) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon |
| ? | NC_000913 | 3423341 = | 35 (1.050) | intergenic (+147/+82) | yhdZ/rrfF | putative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon | |||||
| * | ? | NC_000913 | 3071417 = | 47 (1.310) | 4 (0.120) | 4/232 | 4.1 | 9.1% | intergenic (‑173/+42) | fbaA/pgk | fructose‑bisphosphate aldolase, class II/phosphoglycerate kinase |
| ? | NC_000913 | 3071476 = | 36 (1.070) | coding (1147/1164 nt) | pgk | phosphoglycerate kinase | |||||