Variant ID: vg0809709071 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 9709071 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 101. )
AAGATACAGTAGCGAAGAGATAAGCAGGAGGCACAGGCGACGCCACCCCTGGCCTCTATAAAAGGAGACGTTGGCCTTCACTCCGGGGAGACAGAACCAC[G/A]
AAGACACCATTCAGAGAAAAGCTTCCAAGCGCGCTCTCACCCTCCATTCCATCTTTCTTAGTAGTAGTTCCTCTAGCCTACCTTGCATAATATATATTGA
TCAATATATATTATGCAAGGTAGGCTAGAGGAACTACTACTAAGAAAGATGGAATGGAGGGTGAGAGCGCGCTTGGAAGCTTTTCTCTGAATGGTGTCTT[C/T]
GTGGTTCTGTCTCCCCGGAGTGAAGGCCAACGTCTCCTTTTATAGAGGCCAGGGGTGGCGTCGCCTGTGCCTCCTGCTTATCTCTTCGCTACTGTATCTT
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 | 42.40% | 41.20% | 11.47% | 4.87% | NA |
All Indica | 2759 | 65.70% | 22.60% | 11.27% | 0.40% | NA |
All Japonica | 1512 | 2.40% | 82.90% | 0.99% | 13.76% | NA |
Aus | 269 | 42.80% | 3.70% | 53.16% | 0.37% | NA |
Indica I | 595 | 82.90% | 16.80% | 0.34% | 0.00% | NA |
Indica II | 465 | 47.10% | 17.40% | 34.19% | 1.29% | NA |
Indica III | 913 | 64.30% | 27.70% | 7.89% | 0.11% | NA |
Indica Intermediate | 786 | 65.40% | 24.20% | 9.92% | 0.51% | NA |
Temperate Japonica | 767 | 2.00% | 94.30% | 1.30% | 2.48% | NA |
Tropical Japonica | 504 | 2.40% | 65.70% | 0.20% | 31.75% | NA |
Japonica Intermediate | 241 | 3.70% | 82.60% | 1.66% | 12.03% | NA |
VI/Aromatic | 96 | 12.50% | 12.50% | 66.67% | 8.33% | NA |
Intermediate | 90 | 33.30% | 54.40% | 10.00% | 2.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0809709071 | G -> A | LOC_Os08g15940.1 | upstream_gene_variant ; 2852.0bp to feature; MODIFIER | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
vg0809709071 | G -> A | LOC_Os08g15960.1 | upstream_gene_variant ; 1882.0bp to feature; MODIFIER | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
vg0809709071 | G -> A | LOC_Os08g15930.1 | downstream_gene_variant ; 4932.0bp to feature; MODIFIER | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
vg0809709071 | G -> A | LOC_Os08g15950.1 | downstream_gene_variant ; 787.0bp to feature; MODIFIER | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
vg0809709071 | G -> A | LOC_Os08g15950-LOC_Os08g15960 | intergenic_region ; MODIFIER | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
vg0809709071 | G -> DEL | N | N | silent_mutation | Average:24.46; most accessible tissue: Zhenshan97 root, score: 62.394 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0809709071 | NA | 1.16E-10 | mr1595_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 |
vg0809709071 | NA | 8.65E-12 | mr1600_2 | 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 |