Variant ID: vg0405209631 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 5209631 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AATTGTTATTTGATGTTAAATCAGTGGGTTCTGTCAAGTTAGCTATAGGTTGTGTCATATCAACGATTTCTATGGAAGGTAATAAGATATTATCTTCAGC[A/G]
GTTATGTATCTAGGACCTTTGACAAAAATTGATGCGTTTCTAACTCCACAAAGATTACTTCTCAATATAATTTCTTTCAAATTTAGTAAAATTTCTTTTA
TAAAAGAAATTTTACTAAATTTGAAAGAAATTATATTGAGAAGTAATCTTTGTGGAGTTAGAAACGCATCAATTTTTGTCAAAGGTCCTAGATACATAAC[T/C]
GCTGAAGATAATATCTTATTACCTTCCATAGAAATCGTTGATATGACACAACCTATAGCTAACTTGACAGAACCCACTGATTTAACATCAAATAACAATT
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 | 92.20% | 7.80% | 0.02% | 0.00% | NA |
All Indica | 2759 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 79.70% | 20.20% | 0.07% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 56.30% | 43.50% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 82.20% | 17.80% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0405209631 | A -> G | LOC_Os04g09710.1 | upstream_gene_variant ; 3806.0bp to feature; MODIFIER | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0405209631 | A -> G | LOC_Os04g09720.2 | downstream_gene_variant ; 341.0bp to feature; MODIFIER | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
vg0405209631 | A -> G | LOC_Os04g09720.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0405209631 | NA | 1.67E-18 | mr1301 | 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 |
vg0405209631 | NA | 1.82E-06 | mr1602 | 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 |
vg0405209631 | 6.49E-07 | NA | mr1631 | 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 |