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 37 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,711,947 | 0 | G | A | 53.4% | 43.4 / 179.2 | 119 | Q21* (CAG→TAG) | yhjX | putative transporter YhjX |
| * | NC_000913 | 1,351,463 | 0 | C | A | 36.1% | 93.3 / 12.9 | 72 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.9% | 141.0 / 36.8 | 104 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,477,265 | 0 | A | C | 34.7% | 114.2 / 21.9 | 72 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 4,296,268 | 0 | T | C | 32.6% | 66.8 / 38.9 | 46 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,922,815 | 0 | C | A | 32.1% | 118.4 / 27.8 | 84 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.8% | 248.6 / 17.8 | 132 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 2,767,443 | 0 | C | A | 31.6% | 189.7 / 17.7 | 97 | intergenic (+88/‑267) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 4,296,191 | 0 | A | C | 31.6% | 26.8 / 20.7 | 38 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,334,966 | 0 | A | C | 31.1% | 193.9 / 42.4 | 148 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 4,540,411 | 0 | C | A | 30.4% | 343.3 / 16.8 | 172 | intergenic (‑910/‑546) | nanC/fimB | N‑acetylneuraminate outer membrane channel/Type 1 fimbriae regulatory protein FimB |
| * | NC_000913 | 2,159,413 | 0 | C | T | 30.2% | 71.3 / 12.1 | 43 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 147,802 | 0 | C | A | 30.2% | 208.1 / 16.4 | 116 | R279R (CGG→AGG) | rpnC | recombination‑promoting nuclease RpnC |
| * | NC_000913 | 1,902,613 | 0 | C | A | 30.1% | 147.9 / 12.1 | 73 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 1,097,118 | 0 | C | A | 29.4% | 39.7 / 20.1 | 34 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,841,663 | 0 | G | A | 28.6% | 138.5 / 18.3 | 70 | A26V (GCG→GTG) | nepI | purine ribonucleoside exporter |
| * | NC_000913 | 2,895,349 | 0 | G | T | 28.3% | 180.4 / 10.9 | 99 | P144Q (CCG→CAG) | ygcQ | putative flavoprotein |
| * | NC_000913 | 3,741,871 | 0 | G | T | 27.8% | 186.1 / 19.2 | 108 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 3,431,396 | 0 | C | A | 27.6% | 194.4 / 19.3 | 105 | R7I (AGA→ATA) | tsaC | L‑threonylcarbamoyladenylate synthase |
| * | NC_000913 | 1,502,772 | 0 | G | A | 27.6% | 148.0 / 24.9 | 88 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| Marginal new junction evidence (lowest skew 10 of 23 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 158 (1.630) | 31 (0.330) | 25/580 | 2.5 | 18.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 119 (1.260) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 167 (1.720) | 25 (0.270) | 22/580 | 3.0 | 15.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 119 (1.260) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 23 (0.240) | 20/598 | 3.4 | 20.2% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3710930 = | 91 (0.940) | coding (1078/1209 nt) | yhjX | putative transporter YhjX | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 20 (0.210) | 19/598 | 3.6 | 17.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3710938 | 92 (0.950) | coding (1070/1209 nt) | yhjX | putative transporter YhjX | |||||
| * | ? | NC_000913 | = 696741 | 52 (0.540) | 11 (0.150) | 11/442 | 4.1 | 20.9% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 45 (0.630) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 291401 | NA (NA) | 12 (0.120) | 10/598 | 5.8 | 11.7% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3710930 = | 91 (0.940) | coding (1078/1209 nt) | yhjX | putative transporter YhjX | |||||
| * | ? | NC_000913 | = 2947467 | 67 (0.690) | 5 (0.070) | 5/432 | 6.2 | 8.8% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 55 (0.780) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 1050545 | NA (NA) | 9 (0.090) | 9/598 | 6.2 | 8.9% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3710938 | 92 (0.950) | coding (1070/1209 nt) | yhjX | putative transporter YhjX | |||||
| * | ? | NC_000913 | = 780629 | 100 (1.030) | 5 (0.070) | 5/446 | 6.4 | 7.1% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 56 (0.770) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 7 (0.070) | 7/598 | 6.9 | 4.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4525320 | 151 (1.550) | coding (484/789 nt) | yjhI | putative DNA‑binding transcriptional regulator YjhI | |||||