| Variant ID: vg1101255057 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1255057 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AAAAACAAATGTGAGGACTGCATCGTCTCAAGGAGTAAACTAGTAACAAAATGAAATATTGTTAAGTTACTTATTTTGTCCTCGTATCAATTTGTTGTGT[C/G]
ATGTAGATATTAGTAATAGCAATAATGGATCCCATGCTTCGGATGATGCACATAACAGTATCCTTACTGCAAAGAGAAGACGTTCTACTCAACCTAATTT
AAATTAGGTTGAGTAGAACGTCTTCTCTTTGCAGTAAGGATACTGTTATGTGCATCATCCGAAGCATGGGATCCATTATTGCTATTACTAATATCTACAT[G/C]
ACACAACAAATTGATACGAGGACAAAATAAGTAACTTAACAATATTTCATTTTGTTACTAGTTTACTCCTTGAGACGATGCAGTCCTCACATTTGTTTTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 2.60% | 8.27% | 55.65% | NA |
| All Indica | 2759 | 5.70% | 0.10% | 6.52% | 87.64% | NA |
| All Japonica | 1512 | 89.20% | 7.10% | 1.46% | 2.31% | NA |
| Aus | 269 | 1.90% | 4.10% | 59.11% | 34.94% | NA |
| Indica I | 595 | 5.40% | 0.00% | 10.42% | 84.20% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.51% | 92.69% | NA |
| Indica III | 913 | 1.60% | 0.10% | 5.59% | 92.66% | NA |
| Indica Intermediate | 786 | 10.70% | 0.30% | 7.63% | 81.42% | NA |
| Temperate Japonica | 767 | 93.10% | 2.90% | 2.22% | 1.83% | NA |
| Tropical Japonica | 504 | 95.00% | 2.40% | 0.20% | 2.38% | NA |
| Japonica Intermediate | 241 | 64.30% | 30.30% | 1.66% | 3.73% | NA |
| VI/Aromatic | 96 | 27.10% | 1.00% | 27.08% | 44.79% | NA |
| Intermediate | 90 | 50.00% | 1.10% | 4.44% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101255057 | C -> DEL | N | N | silent_mutation | Average:4.678; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1101255057 | C -> G | LOC_Os11g03340.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.678; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1101255057 | C -> G | LOC_Os11g03330.1 | downstream_gene_variant ; 1077.0bp to feature; MODIFIER | silent_mutation | Average:4.678; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |