Variant ID: vg0711420049 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 11420049 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 122. )
GTGGTTGGCGACTCCATATCACCGCAAGGCGTTTAGGTGTTGCGATCGTGCTTGTCGACTTGTCAAAAAAGTTGCCAACACGATTTTTGGCGACTCCGCT[G/A]
GGGACTAGATCTACATATTACGGCCGAATTTGCTTTAACCTAGTCGCTTCGTCGAATTAATAGTTTCGGCCAAGCGGCCGAAATTAATCTACGCATCACG
CGTGATGCGTAGATTAATTTCGGCCGCTTGGCCGAAACTATTAATTCGACGAAGCGACTAGGTTAAAGCAAATTCGGCCGTAATATGTAGATCTAGTCCC[C/T]
AGCGGAGTCGCCAAAAATCGTGTTGGCAACTTTTTTGACAAGTCGACAAGCACGATCGCAACACCTAAACGCCTTGCGGTGATATGGAGTCGCCAACCAC
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 | 53.60% | 8.40% | 34.49% | 3.55% | NA |
All Indica | 2759 | 27.80% | 9.50% | 57.09% | 5.65% | NA |
All Japonica | 1512 | 94.40% | 4.50% | 0.66% | 0.46% | NA |
Aus | 269 | 76.20% | 17.10% | 6.32% | 0.37% | NA |
Indica I | 595 | 38.50% | 2.40% | 53.45% | 5.71% | NA |
Indica II | 465 | 15.50% | 12.30% | 65.16% | 7.10% | NA |
Indica III | 913 | 21.70% | 12.60% | 60.13% | 5.59% | NA |
Indica Intermediate | 786 | 34.00% | 9.70% | 51.53% | 4.83% | NA |
Temperate Japonica | 767 | 98.30% | 0.10% | 0.78% | 0.78% | NA |
Tropical Japonica | 504 | 86.70% | 12.70% | 0.60% | 0.00% | NA |
Japonica Intermediate | 241 | 97.90% | 1.20% | 0.41% | 0.41% | NA |
VI/Aromatic | 96 | 83.30% | 8.30% | 8.33% | 0.00% | NA |
Intermediate | 90 | 60.00% | 13.30% | 22.22% | 4.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0711420049 | G -> DEL | N | N | silent_mutation | Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
vg0711420049 | G -> A | LOC_Os07g19300.1 | upstream_gene_variant ; 507.0bp to feature; MODIFIER | silent_mutation | Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
vg0711420049 | G -> A | LOC_Os07g19290.1 | downstream_gene_variant ; 512.0bp to feature; MODIFIER | silent_mutation | Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
vg0711420049 | G -> A | LOC_Os07g19290-LOC_Os07g19300 | intergenic_region ; MODIFIER | silent_mutation | Average:30.395; most accessible tissue: Zhenshan97 flower, score: 45.068 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0711420049 | 2.47E-06 | NA | mr1890 | 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 |