mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 28 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,054,894 | 0 | G | T | 42.0% | 105.0 / 46.6 | 100 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,136,467 | 0 | A | C | 36.4% | 62.1 / 23.2 | 55 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 3,054,886 | 0 | G | T | 35.4% | 138.3 / 38.7 | 99 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 847,955 | 0 | G | A | 34.0% | 122.9 / 40.9 | 97 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,097,118 | 0 | C | A | 31.2% | 48.7 / 11.4 | 32 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,922,815 | 0 | C | A | 31.0% | 136.2 / 15.8 | 87 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,990,480 | 0 | C | A | 29.8% | 292.8 / 25.5 | 188 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,054,937 | 0 | G | A | 29.4% | 168.7 / 11.5 | 86 | L170L (CTG→TTG) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,097,158 | 0 | C | T | 29.2% | 25.0 / 10.7 | 24 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 4,296,268 | 0 | T | C | 29.1% | 60.2 / 40.9 | 56 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,185,849 | 0 | G | T | 27.4% | 219.1 / 15.3 | 113 | intergenic (‑53/‑68) | rcnR/rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| * | NC_000913 | 1,334,966 | 0 | A | C | 27.1% | 187.0 / 25.7 | 119 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 58,065 | 0 | C | A | 26.9% | 129.6 / 14.4 | 78 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 1,902,613 | 0 | C | A | 25.7% | 144.6 / 11.5 | 70 | S189Y (TCC→TAC) | manX | mannose‑specific PTS enzyme IIAB component |
| * | NC_000913 | 3,911,533 | 0 | C | A | 25.2% | 261.3 / 11.2 | 139 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,466,432 | 0 | A | G | 25.0% | 64.5 / 21.3 | 44 | pseudogene (1041/2518 nt) | ydbA | putative outer membrane protein, N‑terminal fragment |
| * | NC_000913 | 3,191,376 | 0 | G | T | 23.7% | 320.0 / 18.6 | 152 | E249* (GAG→TAG) | yqiI | putative fimbrial protein YqiI |
| * | NC_000913 | 3,602,706 | 0 | C | A | 23.5% | 114.0 / 24.2 | 68 | G14G (GGG→GGT) | ftsE | cell division protein FtsE |
| * | NC_000913 | 4,296,190 | 0 | A | G | 23.1% | 54.2 / 17.4 | 39 | intergenic (+396/+246) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,054,907 | 0 | G | T | 22.7% | 203.5 / 10.8 | 97 | Q180K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 168 (1.920) | 15 (0.180) | 14/580 | 3.8 | 9.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 129 (1.520) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 159 (1.820) | 16 (0.190) | 13/580 | 4.0 | 10.1% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 130 (1.540) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4606166 | 88 (1.010) | 8 (0.130) | 7/420 | 4.4 | 12.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 53 (0.860) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 2653419 | 73 (0.840) | 8 (0.100) | 8/548 | 5.2 | 9.6% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 83 (1.040) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 4295870 | 65 (0.740) | 7 (0.090) | 7/520 | 5.3 | 9.1% | intergenic (+76/+566) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| ? | NC_000913 | 4296434 = | 84 (1.110) | intergenic (+640/+2) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO | |||||
| * | ? | NC_000913 | = 1286906 | 33 (0.380) | 7 (0.090) | 7/558 | 5.6 | 16.5% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 40 (0.490) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 721951 | 72 (0.820) | 4 (0.050) | 4/574 | 7.0 | 6.4% | coding (2464/2685 nt) | kdpD | sensor histidine kinase KdpD |
| ? | NC_000913 | 722313 = | 47 (0.560) | coding (2102/2685 nt) | kdpD | sensor histidine kinase KdpD | |||||
| * | ? | NC_000913 | = 1287084 | 43 (0.490) | 3 (0.040) | 3/558 | 7.4 | 7.0% | noncoding (153/171 nt) | rttR | small RNA RttR |
| ? | NC_000913 | 1287557 = | 40 (0.490) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||