mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 247 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,151,689 | 0 | G | T | 57.1% | 6.9 / 14.0 | 35 | intergenic (+43/+22) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 2,151,686 | 0 | G | T | 55.9% | ‑4.3 / 19.3 | 35 | intergenic (+40/+25) | yegJ/yegK | uncharacterized protein/ser/thr phosphatase‑related protein |
| * | NC_000913 | 417,533 | 0 | T | G | 45.6% | 40.9 / 21.0 | 57 | V131G (GTG→GGG) | phoB | response regulator in two‑component regulatory system with PhoR |
| * | NC_000913 | 3,862,664 | 0 | C | G | 43.8% | 19.0 / 22.2 | 49 | pseudogene (940/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 811,721 | 0 | T | G | 38.1% | 145.0 / 12.7 | 87 | V67G (GTG→GGG) | bioC | malonyl‑ACP O‑methyltransferase, SAM‑dependent |
| * | NC_000913 | 3,862,668 | 0 | A | G | 37.5% | 59.5 / 10.2 | 48 | pseudogene (936/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 4,442,162 | 0 | A | T | 35.0% | 245.8 / 42.3 | 117 | D5E (GAT→GAA) | msrA | methionine sulfoxide reductase A |
| * | NC_000913 | 249,538 | 0 | T | G | 33.8% | 106.7 / 11.7 | 78 | pseudogene (533/1713 nt) | lfhA | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| * | NC_000913 | 3,665,702 | 0 | C | A | 33.7% | 221.5 / 45.2 | 92 | A37S (GCG→TCG) | gadX | acid resistance regulon transcriptional activator; autoactivator |
| * | NC_000913 | 2,228,275 | 0 | T | C | 32.7% | 105.9 / 14.5 | 56 | pseudogene (335/1287 nt) | mdtQ | pseudogene; putative channel/filament proteins |
| * | NC_000913 | 3,862,677 | 0 | G | A | 32.6% | 29.7 / 13.4 | 48 | pseudogene (927/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| * | NC_000913 | 4,604,350 | 0 | C | T | 32.2% | 231.8 / 53.0 | 121 | S64F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 433,634 | 0 | T | G | 31.7% | 121.4 / 26.0 | 104 | G60G (GGT→GGG) | ribD | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| * | NC_000913 | 1,265,473 | 0 | T | G | 31.6% | 185.6 / 14.6 | 76 | G154G (GGT→GGG) | prfA | peptide chain release factor RF‑1 |
| * | NC_000913 | 4,604,344 | 0 | C | T | 31.4% | 229.9 / 55.9 | 121 | S62F (TCT→TTT) | bglJ | bgl operon transcriptional activator |
| * | NC_000913 | 954,388 | 0 | C | T | 31.3% | 93.1 / 20.8 | 68 | A27T (GCA→ACA) | focA | formate channel |
| * | NC_000913 | 3,745,397 | 0 | A | C | 31.2% | 183.1 / 14.3 | 93 | L198F (TTA→TTC) | yiaN | 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein |
| * | NC_000913 | 1,335,705 | 0 | G | T | 30.6% | 337.1 / 34.5 | 135 | intergenic (+247/‑126) | yciX/acnA | uncharacterized protein/aconitate hydratase 1; aconitase A |
| * | NC_000913 | 1,383,722 | 0 | G | A | 30.4% | 215.7 / 47.6 | 118 | F80F (TTC→TTT) | ycjW | LacI family putative transcriptional repressor |
| * | NC_000913 | 3,844,219 | 0 | T | G | 30.3% | 251.6 / 15.4 | 99 | F86V (TTT→GTT) | adeD | cryptic adenine deaminase |
| Marginal new junction evidence (lowest skew 10 of 68 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1387098 | 135 (0.820) | 11 (0.070) | 10/318 | 9.0 | 8.1% | coding (379/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| ? | NC_000913 | = 1387248 | 121 (0.760) | coding (529/1542 nt) | tyrR | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase | |||||
| * | ? | NC_000913 | = 2357690 | 136 (0.820) | 7 (0.050) | 6/280 | 9.9 | 5.4% | coding (787/900 nt) | yfaD | transposase_31 family protein |
| ? | NC_000913 | 2357874 = | 128 (0.910) | pseudogene (71/198 nt) | ypaA | pseudogene, C‑terminal fragment, Transposase_31 family | |||||
| * | ? | NC_000913 | 2077808 = | 234 (1.410) | 9 (0.060) | 7/306 | 10.0 | 3.9% | coding (240/375 nt) | cbtA | CP4‑44 prophage; toxin of the YeeV‑YeeU toxin‑antitoxin system |
| ? | NC_000913 | 2077982 = | 227 (1.480) | pseudogene (43/168 nt) | yeeW | CP4‑44 prophage; uncharacterized protein;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 315401 = | NA (NA) | 8 (0.050) | 7/304 | 10.0 | NA | noncoding (173/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315627 = | NA (NA) | noncoding (399/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 2791557 | 118 (0.710) | 6 (0.040) | 6/308 | 10.5 | 5.0% | coding (285/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| ? | NC_000913 | = 2791668 | 118 (0.760) | coding (396/1449 nt) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent | |||||
| * | ? | NC_000913 | 1200223 = | 185 (1.120) | 6 (0.040) | 6/308 | 10.5 | 3.0% | coding (584/1128 nt) | intE | e14 prophage; putative integrase |
| ? | NC_000913 | 1200424 = | 209 (1.350) | coding (383/1128 nt) | intE | e14 prophage; putative integrase | |||||
| * | ? | NC_000913 | = 711718 | 223 (1.350) | 8 (0.050) | 6/322 | 10.8 | 3.9% | coding (181/294 nt) | ybfE | LexA‑regulated protein, CopB family |
| ? | NC_000913 | = 712015 | 181 (1.120) | intergenic (‑117/+23) | ybfE/ybfF | LexA‑regulated protein, CopB family/acyl‑CoA esterase | |||||
| * | ? | NC_000913 | = 818767 | 223 (1.350) | 5 (0.030) | 5/310 | 11.1 | 2.6% | coding (198/486 nt) | moaC | molybdopterin biosynthesis, protein C |
| ? | NC_000913 | = 818875 | 165 (1.060) | coding (306/486 nt) | moaC | molybdopterin biosynthesis, protein C | |||||
| * | ? | NC_000913 | = 2883773 | 166 (1.000) | 5 (0.030) | 5/314 | 11.2 | 3.2% | coding (366/1509 nt) | casA | CRISP RNA (crRNA) containing Cascade antiviral complex protein |
| ? | NC_000913 | = 2883880 | 144 (0.910) | coding (259/1509 nt) | casA | CRISP RNA (crRNA) containing Cascade antiviral complex protein | |||||
| * | ? | NC_000913 | = 2066696 | 221 (1.330) | 6 (0.040) | 5/318 | 11.3 | 2.7% | noncoding (658/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2102175 | NA (NA) | noncoding (769/1195 nt) | IS5 | repeat region | |||||