Variant ID: vg0820093707 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 20093707 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 122. )
TCCGTTCCTCAACCAACCAGAGACCGACGACGGCCGGCGGCACAACGAGCTTCAACCTACGGAGGCCGACAGCTCCCCAACCTCCGCCCAACCACAAGTC[G/A]
CAGGAGGCCAATGACAATTCCACTGATAACGGCCGGCAGCTCAAGCTACCCCGTCATCGTGTCATTGCTTCACCATGGCCTCCTCTCCCCTCTCCCCGTG
CACGGGGAGAGGGGAGAGGAGGCCATGGTGAAGCAATGACACGATGACGGGGTAGCTTGAGCTGCCGGCCGTTATCAGTGGAATTGTCATTGGCCTCCTG[C/T]
GACTTGTGGTTGGGCGGAGGTTGGGGAGCTGTCGGCCTCCGTAGGTTGAAGCTCGTTGTGCCGCCGGCCGTCGTCGGTCTCTGGTTGGTTGAGGAACGGA
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 | 85.60% | 14.40% | 0.02% | 0.00% | NA |
All Indica | 2759 | 77.10% | 22.80% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 87.00% | 13.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 83.70% | 16.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 88.40% | 11.40% | 0.22% | 0.00% | NA |
Indica III | 913 | 63.50% | 36.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 81.30% | 18.70% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 88.90% | 11.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0820093707 | G -> A | LOC_Os08g32450.1 | upstream_gene_variant ; 103.0bp to feature; MODIFIER | silent_mutation | Average:63.153; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
vg0820093707 | G -> A | LOC_Os08g32460.1 | upstream_gene_variant ; 1976.0bp to feature; MODIFIER | silent_mutation | Average:63.153; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
vg0820093707 | G -> A | LOC_Os08g32440.1 | downstream_gene_variant ; 2842.0bp to feature; MODIFIER | silent_mutation | Average:63.153; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
vg0820093707 | G -> A | LOC_Os08g32440-LOC_Os08g32450 | intergenic_region ; MODIFIER | silent_mutation | Average:63.153; most accessible tissue: Zhenshan97 young leaf, score: 78.044 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0820093707 | 1.21E-06 | 1.21E-06 | mr1463 | 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 |
vg0820093707 | 7.52E-06 | 7.52E-06 | mr1463 | 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 |
vg0820093707 | NA | 7.75E-07 | mr1574 | 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 |
vg0820093707 | NA | 6.20E-06 | mr1138_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 |
vg0820093707 | NA | 7.87E-06 | mr1403_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 |