Variant ID: vg0704593047 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 4593047 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )
ACAGGATGTGTACTTTGGCCAGCCCGCCCGACTGACTATACATAATTCAACAATTACAGCTTGCACCTATTTATTCCATTCTAAAACTATAAAATTTGCT[T/A]
AAAACAAATTTTTTACCATGTAGACCACAAAAGCATTTATAAACTATTATATTGAAGCCACATCAGAGTGTTCTATTATAGCTGCAAGTAGTCTTGGCAT
ATGCCAAGACTACTTGCAGCTATAATAGAACACTCTGATGTGGCTTCAATATAATAGTTTATAAATGCTTTTGTGGTCTACATGGTAAAAAATTTGTTTT[A/T]
AGCAAATTTTATAGTTTTAGAATGGAATAAATAGGTGCAAGCTGTAATTGTTGAATTATGTATAGTCAGTCGGGCGGGCTGGCCAAAGTACACATCCTGT
Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 81.00% | 18.80% | 0.15% | 0.00% | NA |
All Indica | 2759 | 99.40% | 0.50% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 43.60% | 56.00% | 0.40% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.20% | 0.17% | 0.00% | NA |
Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 55.10% | 44.20% | 0.65% | 0.00% | NA |
Tropical Japonica | 504 | 35.30% | 64.70% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 24.10% | 75.50% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 70.00% | 30.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0704593047 | T -> A | LOC_Os07g08850.1 | downstream_gene_variant ; 2381.0bp to feature; MODIFIER | silent_mutation | Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
vg0704593047 | T -> A | LOC_Os07g08860.1 | downstream_gene_variant ; 47.0bp to feature; MODIFIER | silent_mutation | Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
vg0704593047 | T -> A | LOC_Os07g08870.1 | downstream_gene_variant ; 3359.0bp to feature; MODIFIER | silent_mutation | Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
vg0704593047 | T -> A | LOC_Os07g08850-LOC_Os07g08860 | intergenic_region ; MODIFIER | silent_mutation | Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0704593047 | NA | 3.24E-14 | mr1905 | 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 |
vg0704593047 | NA | 1.64E-07 | mr1623_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 |