Variant ID: vg0827379782 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 27379782 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 126. )
ACTGATATATATACTGAGATTAATAAAGTCATTATAGGTATCTCATAGTCGACGGGTATGTCACTTACCACTAAAAGAATAATTAGTCGTAAATATAACT[A/G]
TATAAGCATCAGTATCAAGTCTAACACTTGAACCCAGATAGGTCACCTAAAAAATATAATCAGTTAAGCTACGCTCACTTCGCCGCTCAATTAATAATTT
AAATTATTAATTGAGCGGCGAAGTGAGCGTAGCTTAACTGATTATATTTTTTAGGTGACCTATCTGGGTTCAAGTGTTAGACTTGATACTGATGCTTATA[T/C]
AGTTATATTTACGACTAATTATTCTTTTAGTGGTAAGTGACATACCCGTCGACTATGAGATACCTATAATGACTTTATTAATCTCAGTATATATATCAGT
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 | 91.40% | 8.60% | 0.02% | 0.00% | NA |
All Indica | 2759 | 85.70% | 14.30% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 91.90% | 8.10% | 0.00% | 0.00% | NA |
Indica II | 465 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
Indica III | 913 | 75.20% | 24.60% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 10.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0827379782 | A -> G | LOC_Os08g43320.1 | upstream_gene_variant ; 747.0bp to feature; MODIFIER | silent_mutation | Average:68.365; most accessible tissue: Callus, score: 85.438 | N | N | N | N |
vg0827379782 | A -> G | LOC_Os08g43334.1 | downstream_gene_variant ; 983.0bp to feature; MODIFIER | silent_mutation | Average:68.365; most accessible tissue: Callus, score: 85.438 | N | N | N | N |
vg0827379782 | A -> G | LOC_Os08g43334.2 | downstream_gene_variant ; 3083.0bp to feature; MODIFIER | silent_mutation | Average:68.365; most accessible tissue: Callus, score: 85.438 | N | N | N | N |
vg0827379782 | A -> G | LOC_Os08g43320-LOC_Os08g43334 | intergenic_region ; MODIFIER | silent_mutation | Average:68.365; most accessible tissue: Callus, score: 85.438 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0827379782 | 6.41E-06 | 1.28E-07 | mr1004_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 |
vg0827379782 | NA | 7.67E-06 | mr1004_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 |