Variant ID: vg1106988724 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 6988724 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )
TAACAACAACCTCTCCCCCTCAAAACACAAGATCACACATCCCAATGGGGCTCTGCCCCATGACACCCAGAATGCACTTCAGCGGTACATGTTCGACTCT[G/A]
TGTTTTGAACAACGTTTGTAAAAACTACAGAAAAACACCCCCCTCCCATTTATTTTTAAATAAAAAAAGCTTGAAATGATCACAAAATCTAAAGAAAGAA
TTCTTTCTTTAGATTTTGTGATCATTTCAAGCTTTTTTTATTTAAAAATAAATGGGAGGGGGGTGTTTTTCTGTAGTTTTTACAAACGTTGTTCAAAACA[C/T]
AGAGTCGAACATGTACCGCTGAAGTGCATTCTGGGTGTCATGGGGCAGAGCCCCATTGGGATGTGTGATCTTGTGTTTTGAGGGGGAGAGGTTGTTGTTA
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 75.30% | 3.00% | 5.56% | 16.17% | NA |
All Indica | 2759 | 97.20% | 0.20% | 0.83% | 1.78% | NA |
All Japonica | 1512 | 32.10% | 8.50% | 14.22% | 45.24% | NA |
Aus | 269 | 98.90% | 0.70% | 0.00% | 0.37% | NA |
Indica I | 595 | 98.70% | 0.20% | 0.84% | 0.34% | NA |
Indica II | 465 | 98.90% | 0.20% | 0.22% | 0.65% | NA |
Indica III | 913 | 95.60% | 0.30% | 0.66% | 3.40% | NA |
Indica Intermediate | 786 | 96.80% | 0.10% | 1.40% | 1.65% | NA |
Temperate Japonica | 767 | 32.10% | 1.00% | 8.34% | 58.54% | NA |
Tropical Japonica | 504 | 31.00% | 21.60% | 19.44% | 27.98% | NA |
Japonica Intermediate | 241 | 34.40% | 4.60% | 21.99% | 39.00% | NA |
VI/Aromatic | 96 | 54.20% | 4.20% | 20.83% | 20.83% | NA |
Intermediate | 90 | 83.30% | 0.00% | 5.56% | 11.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1106988724 | G -> A | LOC_Os11g12490.1 | downstream_gene_variant ; 2845.0bp to feature; MODIFIER | silent_mutation | Average:30.912; most accessible tissue: Callus, score: 48.908 | N | N | N | N |
vg1106988724 | G -> A | LOC_Os11g12510.1 | downstream_gene_variant ; 2290.0bp to feature; MODIFIER | silent_mutation | Average:30.912; most accessible tissue: Callus, score: 48.908 | N | N | N | N |
vg1106988724 | G -> A | LOC_Os11g12500.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.912; most accessible tissue: Callus, score: 48.908 | N | N | N | N |
vg1106988724 | G -> DEL | N | N | silent_mutation | Average:30.912; most accessible tissue: Callus, score: 48.908 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1106988724 | 1.24E-06 | 1.24E-06 | mr1098 | Jap_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 |
vg1106988724 | 8.51E-06 | 5.78E-07 | mr1101 | Jap_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 |
vg1106988724 | 3.34E-06 | 3.34E-06 | mr1589 | Jap_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 |