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 43 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 339,986 | 0 | G | A | 74.3% | 55.3 / 20.3 | 35 | R73Q (CGA→CAA) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 339,979 | 0 | G | A | 69.4% | 45.7 / 27.6 | 37 | V71M (GTG→ATG) | yahH | putative uncharacterized protein YahH |
| * | NC_000913 | 4,296,191 | 0 | A | C | 34.2% | 25.3 / 29.3 | 41 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,922,815 | 0 | C | A | 33.7% | 163.0 / 15.4 | 98 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,767,445 | 0 | C | A | 33.3% | 184.6 / 10.5 | 94 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 1,427,992 | 0 | G | T | 32.2% | 187.5 / 10.5 | 121 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 2,477,265 | 0 | A | C | 31.6% | 136.4 / 23.4 | 79 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 3,054,886 | 0 | G | T | 31.6% | 129.5 / 21.0 | 76 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,444 | 0 | C | A | 31.5% | 187.8 / 11.9 | 94 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,767,449 | 0 | C | A | 31.0% | 210.1 / 11.9 | 101 | intergenic (+94/‑261) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.9% | 194.8 / 25.4 | 123 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 4,296,268 | 0 | T | C | 30.2% | 54.9 / 33.3 | 43 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,288,418 | 0 | G | T | 30.1% | 236.5 / 26.2 | 133 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 1,334,966 | 0 | A | C | 29.4% | 260.7 / 32.3 | 154 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,054,894 | 0 | G | T | 29.3% | 120.4 / 18.8 | 75 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 4,136,467 | 0 | A | C | 28.8% | 85.5 / 13.1 | 53 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 4,360,965 | 0 | C | A | 28.8% | 274.8 / 25.4 | 139 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,159,413 | 0 | C | T | 27.7% | 81.2 / 12.4 | 47 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 4,427,822 | 0 | C | A | 27.5% | 245.4 / 12.0 | 131 | intergenic (‑400/+257) | yjfZ/ytfB | DUF2686 domain‑containing protein YjfZ/cell division protein YtfB |
| * | NC_000913 | 2,013,023 | 0 | C | A | 27.1% | 160.3 / 13.0 | 96 | intergenic (‑9/‑206) | fliE/fliF | flagellar protein FliE/flagellar basal‑body MS‑ring and collar protein |
| Marginal new junction evidence (lowest skew 10 of 25 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4542690 | 144 (1.470) | 25 (0.260) | 21/580 | 3.8 | 15.9% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 124 (1.300) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | 4542682 = | 142 (1.440) | 19 (0.200) | 16/580 | 4.9 | 12.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 127 (1.330) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 781222 | 48 (0.490) | 12 (0.160) | 11/446 | 4.9 | 20.7% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 56 (0.760) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 2101749 = | NA (NA) | 15 (0.150) | 14/598 | 5.6 | 9.8% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2103587 | 138 (1.400) | coding (923/1119 nt) | wbbK | putative glycosyltransferase WbbK | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 12 (0.120) | 11/598 | 6.6 | 11.0% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4162510 | 97 (0.990) | coding (761/1101 nt) | trmA | tRNA m(5)U54 methyltransferase | |||||
| * | ? | NC_000913 | = 2102943 | NA (NA) | 10 (0.100) | 10/598 | 6.9 | 6.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 2103584 = | 137 (1.390) | coding (926/1119 nt) | wbbK | putative glycosyltransferase WbbK | |||||
| * | ? | NC_000913 | = 4606166 | 81 (0.820) | 5 (0.070) | 5/420 | 7.1 | 8.6% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 49 (0.710) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 1286906 | 71 (0.720) | 11 (0.120) | 7/558 | 7.7 | 13.4% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 76 (0.830) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 2947467 | 76 (0.770) | 4 (0.060) | 4/432 | 7.8 | 5.9% | intergenic (+4/‑30) | metZ/metW | tRNA‑Met/tRNA‑Met |
| ? | NC_000913 | 2947688 = | 72 (1.010) | intergenic (+5/+69) | metV/amiC | tRNA‑Met/N‑acetylmuramoyl‑L‑alanine amidase C | |||||
| * | ? | NC_000913 | = 2521006 | 92 (0.940) | 4 (0.050) | 4/446 | 8.0 | 6.3% | noncoding (76/76 nt) | valU | tRNA‑Val |
| ? | NC_000913 | 2521249 = | 50 (0.680) | intergenic (+1/‑4) | valY/lysV | tRNA‑Val/tRNA‑Lys | |||||