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 36 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,477,265 | 0 | A | C | 35.6% | 132.7 / 34.6 | 87 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,922,815 | 0 | C | A | 35.5% | 139.5 / 28.5 | 93 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 3,054,894 | 0 | G | T | 34.3% | 125.7 / 34.5 | 102 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,602,706 | 0 | C | A | 34.2% | 48.9 / 63.1 | 82 | G14G (GGG→GGT) | ftsE | cell division protein FtsE |
| * | NC_000913 | 58,065 | 0 | C | A | 33.0% | 192.1 / 22.7 | 112 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.9% | 320.9 / 28.8 | 169 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 3,054,886 | 0 | G | T | 31.1% | 183.6 / 30.6 | 106 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,457,177 | 0 | T | G | 31.1% | 67.9 / 10.0 | 47 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| * | NC_000913 | 1,820,763 | 0 | G | T | 30.9% | 136.3 / 14.4 | 94 | S151Y (TCC→TAC) | chbC | N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component |
| * | NC_000913 | 3,741,871 | 0 | G | T | 29.3% | 281.7 / 40.1 | 164 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,136,467 | 0 | A | C | 29.3% | 155.3 / 18.2 | 84 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 1,334,966 | 0 | A | C | 29.1% | 176.1 / 32.8 | 117 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 2,288,418 | 0 | G | T | 28.8% | 262.6 / 20.7 | 132 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 4,213,310 | 0 | G | T | 28.6% | 301.4 / 19.5 | 155 | G26V (GGA→GTA) | yjaA | stress response protein |
| * | NC_000913 | 2,767,445 | 0 | C | A | 27.5% | 226.8 / 12.0 | 102 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,755,936 | 0 | A | C | 27.2% | 203.4 / 12.6 | 92 | noncoding (344/363 nt) | ssrA | tmRNA |
| * | NC_000913 | 847,955 | 0 | G | A | 27.1% | 194.1 / 44.5 | 123 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,097,158 | 0 | C | T | 26.9% | 22.1 / 14.1 | 26 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 4,360,965 | 0 | C | A | 26.9% | 449.3 / 35.6 | 212 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 3,602,698 | 0 | G | A | 26.8% | 156.7 / 15.2 | 82 | A17V (GCG→GTG) | ftsE | cell division protein FtsE |
| Marginal new junction evidence (lowest skew 10 of 15 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 4542682 = | 175 (1.630) | 25 (0.240) | 21/580 | 3.1 | 13.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 139 (1.340) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 185 (1.730) | 17 (0.160) | 15/580 | 4.1 | 9.6% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 139 (1.340) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 3648146 | 187 (1.740) | 13 (0.150) | 11/482 | 4.3 | 8.6% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 126 (1.460) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 4606166 | 238 (2.220) | 8 (0.110) | 8/420 | 4.6 | 4.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 163 (2.160) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 4392437 | 101 (0.940) | 5 (0.060) | 5/442 | 5.9 | 6.3% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 73 (0.920) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 2653419 | 79 (0.740) | 8 (0.080) | 7/548 | 6.0 | 9.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 78 (0.790) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | 4617536 = | 38 (0.350) | 7 (0.070) +GTGGGAAGTTGT |
6/574 | 6.6 | 15.8% | coding (214/780 nt) | deoC | deoxyribose‑phosphate aldolase |
| ? | NC_000913 | = 4617542 | 40 (0.370) | coding (220/780 nt) | deoC | deoxyribose‑phosphate aldolase | |||||
| * | ? | NC_000913 | = 1287084 | 47 (0.440) | 6 (0.060) | 5/558 | 6.8 | 12.5% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 40 (0.400) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | 4617557 = | 31 (0.290) | 5 (0.050) +ATGTGGGAAGTTG |
5/572 | 7.0 | 14.6% | coding (235/780 nt) | deoC | deoxyribose‑phosphate aldolase |
| ? | NC_000913 | = 4617562 | 30 (0.280) | coding (240/780 nt) | deoC | deoxyribose‑phosphate aldolase | |||||
| * | ? | NC_000913 | = 4295870 | 86 (0.800) | 4 (0.040) | 4/520 | 7.0 | 4.9% | intergenic (+76/+566) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296434 = | 82 (0.880) | intergenic (+640/+2) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||