Variant ID: vg0802211662 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 2211662 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, G: 0.22, others allele: 0.00, population size: 204. )
GGATTTCATGGTGGTCAGTACTTTCTTGTAGAAGAACTTCATGTAGCCTGGAAGTTCTTCAGCGGCTTCCTCATCCCATCTATTATATTTTTATGGTTCA[A/G]
TCATTGATAAAAATTAAATTCAAGTTAAAGACAAGAATTTTGGCTCCATGCAGCTTCTTTGAAACAAATTAAGTTCGGAATGAATTTCATTATTAAAAGA
TCTTTTAATAATGAAATTCATTCCGAACTTAATTTGTTTCAAAGAAGCTGCATGGAGCCAAAATTCTTGTCTTTAACTTGAATTTAATTTTTATCAATGA[T/C]
TGAACCATAAAAATATAATAGATGGGATGAGGAAGCCGCTGAAGAACTTCCAGGCTACATGAAGTTCTTCTACAAGAAAGTACTGACCACCATGAAATCC
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 | 58.30% | 41.30% | 0.15% | 0.30% | NA |
All Indica | 2759 | 34.10% | 65.20% | 0.18% | 0.47% | NA |
All Japonica | 1512 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
Aus | 269 | 65.40% | 34.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 39.50% | 60.20% | 0.00% | 0.34% | NA |
Indica II | 465 | 15.50% | 83.90% | 0.43% | 0.22% | NA |
Indica III | 913 | 31.10% | 68.30% | 0.33% | 0.22% | NA |
Indica Intermediate | 786 | 44.50% | 54.50% | 0.00% | 1.02% | NA |
Temperate Japonica | 767 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 61.10% | 35.60% | 2.22% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0802211662 | A -> G | LOC_Os08g04490.1 | downstream_gene_variant ; 1973.0bp to feature; MODIFIER | silent_mutation | Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
vg0802211662 | A -> G | LOC_Os08g04500.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
vg0802211662 | A -> G | LOC_Os08g04500.2 | intron_variant ; MODIFIER | silent_mutation | Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
vg0802211662 | A -> DEL | N | N | silent_mutation | Average:47.005; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0802211662 | NA | 3.65E-07 | mr1593 | 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 |
vg0802211662 | 1.49E-33 | 3.26E-31 | mr1739 | 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 |
vg0802211662 | 9.72E-37 | 1.13E-65 | mr1739 | 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 |
vg0802211662 | NA | 1.10E-06 | mr1268_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 |
vg0802211662 | 1.94E-29 | 8.05E-27 | mr1739_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 |
vg0802211662 | 1.79E-43 | 6.86E-76 | mr1739_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 |