mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 45 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 58,065 | 0 | C | A | 39.1% | 159.7 / 32.5 | 110 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.0% | 141.1 / 33.2 | 94 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,159,413 | 0 | C | T | 33.3% | 49.2 / 13.5 | 36 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 2,767,445 | 0 | C | A | 33.3% | 245.1 / 29.0 | 129 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,722,838 | 0 | G | T | 32.4% | 191.1 / 13.5 | 105 | E38* (GAG→TAG) | pssA | phosphatidylserine synthase |
| * | NC_000913 | 1,902,613 | 0 | C | A | 32.2% | 167.3 / 14.3 | 90 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 4,296,191 | 0 | A | C | 32.1% | 14.9 / 21.3 | 28 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,864,426 | 0 | G | T | 32.0% | 184.1 / 10.9 | 125 | G64V (GGA→GTA) | ygbM | putative 2‑oxo‑tetronate isomerase YgbM |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.1% | 273.3 / 24.0 | 161 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,767,444 | 0 | C | A | 31.0% | 275.8 / 13.8 | 129 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 12,152 | 0 | G | T | 29.9% | 212.1 / 10.6 | 117 | intergenic (‑366/‑11) | yaaI/dnaK | DUF2541 domain‑containing protein YaaI/chaperone protein DnaK |
| * | NC_000913 | 1,015,488 | 0 | C | A | 29.6% | 234.3 / 16.8 | 135 | intergenic (+29/‑227) | pqiC/rmf | intermembrane transport lipoprotein PqiC/ribosome modulation factor |
| * | NC_000913 | 2,477,265 | 0 | A | C | 29.4% | 176.5 / 12.7 | 85 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 878,375 | 0 | G | T | 29.4% | 298.4 / 23.8 | 160 | R43L (CGA→CTA) | bssR | regulator of biofilm formation |
| * | NC_000913 | 1,922,815 | 0 | C | A | 28.3% | 214.1 / 25.5 | 127 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.1% | 223.8 / 14.5 | 121 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 1,097,118 | 0 | C | A | 28.0% | 76.8 / 20.2 | 50 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,073,613 | 0 | G | T | 27.9% | 159.7 / 10.8 | 86 | R692L (CGG→CTG) | flu | self recognizing antigen 43 (Ag43) autotransporter |
| * | NC_000913 | 141,849 | 0 | C | A | 27.1% | 235.9 / 19.4 | 118 | P140Q (CCG→CAG) | hpt | hypoxanthine phosphoribosyltransferase |
| * | NC_000913 | 1,756,353 | 0 | C | A | 26.7% | 248.7 / 14.0 | 120 | S219Y (TCC→TAC) | pykF | pyruvate kinase 1 |
| Marginal new junction evidence (lowest skew 10 of 12 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 166 (1.520) | 22 (0.210) | 21/580 | 4.2 | 12.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 135 (1.280) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 162 (1.490) | 22 (0.210) | 19/580 | 4.7 | 13.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 136 (1.290) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4392437 | 81 (0.740) | 10 (0.120) | 10/442 | 5.6 | 13.4% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 69 (0.860) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 3648146 | 126 (1.160) | 8 (0.090) | 8/482 | 6.9 | 7.4% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 98 (1.120) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 696741 | 77 (0.710) | 6 (0.070) | 6/442 | 7.3 | 8.6% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 70 (0.870) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | 781577 = | 70 (0.640) | 10 (0.090) +GAAG |
9/590 | 7.7 | 11.1% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521006 | 93 (0.850) | noncoding (76/76 nt) | valU | tRNA‑Val | |||||
| * | ? | NC_000913 | = 696505 | 80 (0.730) | 4 (0.040) | 4/538 | 9.6 | 5.7% | intergenic (‑1/+37) | glnX/glnV | tRNA‑Gln/tRNA‑Gln |
| ? | NC_000913 | 696832 = | 61 (0.620) | intergenic (‑2/+33) | glnW/glnU | tRNA‑Gln/tRNA‑Gln | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 4 (0.040) | 4/598 | 10.2 | 2.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1902911 = | 138 (1.270) | coding (864/972 nt) | manX | mannose‑specific PTS enzyme IIAB component | |||||
| * | ? | NC_000913 | 257908 = | NA (NA) | 4 (0.040) | 4/598 | 10.2 | 2.8% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1902911 = | 138 (1.270) | coding (864/972 nt) | manX | mannose‑specific PTS enzyme IIAB component | |||||
| * | ? | NC_000913 | = 2904163 | 96 (0.880) | 6 (0.060) | 3/540 | 10.3 | 5.5% | intergenic (+789/+584) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | 2904408 = | 120 (1.220) | intergenic (+1034/+339) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||