Variant ID: vg0819862457 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 19862457 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACCCTGACAGTAGCCCCCCGACTTCTGCTTAAATGAACTCGTGAGACCGATCGCAACTTCTGATGTCGGAGTTGTCGTTGTTCTCGATGTGAGGACCGA[G/A]
AGACGAGGAGTGATCGACAACGTCGGGTGAAGCTTCAACGGTCATGAGTGAATTTAAATTGAAGTCTGAAAAATTGCCGCGTGTAACGGACCCAGAAATT
AATTTCTGGGTCCGTTACACGCGGCAATTTTTCAGACTTCAATTTAAATTCACTCATGACCGTTGAAGCTTCACCCGACGTTGTCGATCACTCCTCGTCT[C/T]
TCGGTCCTCACATCGAGAACAACGACAACTCCGACATCAGAAGTTGCGATCGGTCTCACGAGTTCATTTAAGCAGAAGTCGGGGGGCTACTGTCAGGGTT
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 | 94.20% | 5.60% | 0.17% | 0.04% | NA |
All Indica | 2759 | 97.80% | 2.10% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Aus | 269 | 27.90% | 68.80% | 2.60% | 0.74% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 95.50% | 4.30% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
Intermediate | 90 | 92.20% | 7.80% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0819862457 | G -> A | LOC_Os08g32010.1 | upstream_gene_variant ; 3004.0bp to feature; MODIFIER | silent_mutation | Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
vg0819862457 | G -> A | LOC_Os08g32020.1 | upstream_gene_variant ; 297.0bp to feature; MODIFIER | silent_mutation | Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
vg0819862457 | G -> A | LOC_Os08g32030.1 | downstream_gene_variant ; 3953.0bp to feature; MODIFIER | silent_mutation | Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
vg0819862457 | G -> A | LOC_Os08g32010-LOC_Os08g32020 | intergenic_region ; MODIFIER | silent_mutation | Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
vg0819862457 | G -> DEL | N | N | silent_mutation | Average:30.854; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0819862457 | 1.43E-07 | NA | mr1248 | 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 |
vg0819862457 | NA | 1.57E-08 | mr1465 | 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 |