| Variant ID: vg0712646803 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 12646803 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGTGTGGGGGAGATATCCCAGCTTCTGACGTGCACATAATCTGAAAATTGCTGAATATTTGAACACCTAGAAGGCACCAAACTCTGCAGCAATTTGCAGA[A/G]
GGATTGGGCACCAGAGTGGTTCGGCCGAACCAAGTCTGGCCCCAAACCCTCTCAACTTTCAATGGTAAACAGGTGAGCACGTCTTTTATCTGTATATCTC
GAGATATACAGATAAAAGACGTGCTCACCTGTTTACCATTGAAAGTTGAGAGGGTTTGGGGCCAGACTTGGTTCGGCCGAACCACTCTGGTGCCCAATCC[T/C]
TCTGCAAATTGCTGCAGAGTTTGGTGCCTTCTAGGTGTTCAAATATTCAGCAATTTTCAGATTATGTGCACGTCAGAAGCTGGGATATCTCCCCCACACT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 41.40% | 7.00% | 20.93% | 30.60% | NA |
| All Indica | 2759 | 9.40% | 11.30% | 33.71% | 45.63% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 1.65% | 1.59% | NA |
| Aus | 269 | 38.30% | 0.40% | 9.67% | 51.67% | NA |
| Indica I | 595 | 2.00% | 2.70% | 22.18% | 73.11% | NA |
| Indica II | 465 | 9.20% | 3.90% | 29.89% | 56.99% | NA |
| Indica III | 913 | 8.00% | 20.90% | 50.16% | 20.92% | NA |
| Indica Intermediate | 786 | 16.50% | 11.10% | 25.57% | 46.82% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.39% | 1.17% | NA |
| Tropical Japonica | 504 | 94.80% | 0.40% | 3.97% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.83% | 4.56% | NA |
| VI/Aromatic | 96 | 86.50% | 12.50% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 58.90% | 6.70% | 7.78% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0712646803 | A -> DEL | N | N | silent_mutation | Average:15.69; most accessible tissue: Callus, score: 38.231 | N | N | N | N |
| vg0712646803 | A -> G | LOC_Os07g22480.1 | downstream_gene_variant ; 259.0bp to feature; MODIFIER | silent_mutation | Average:15.69; most accessible tissue: Callus, score: 38.231 | N | N | N | N |
| vg0712646803 | A -> G | LOC_Os07g22480-LOC_Os07g22494 | intergenic_region ; MODIFIER | silent_mutation | Average:15.69; most accessible tissue: Callus, score: 38.231 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0712646803 | NA | 3.36E-07 | mr1205_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0712646803 | 2.51E-06 | 2.51E-06 | mr1643_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0712646803 | NA | 3.34E-06 | mr1954_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |