Variant ID: vg0906442847 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 6442847 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 103. )
CTATATAGTACATTCAAAAAGAAAACCAGATTATTTCTTCATGCGATTGTTACAATGCTGGGAGACGGTGGATTATTTGAGATTGCTAGTTAAACTGCAT[T/A]
TTCCTCGTGATCTGAAGGAGGAAGAAAAGGTGGCTGCCATCGCCATGGCAGGGTGTAGAGGAATAACTTGAAGCACATTGGAGAAGCTCATGGATTCTAG
CTAGAATCCATGAGCTTCTCCAATGTGCTTCAAGTTATTCCTCTACACCCTGCCATGGCGATGGCAGCCACCTTTTCTTCCTCCTTCAGATCACGAGGAA[A/T]
ATGCAGTTTAACTAGCAATCTCAAATAATCCACCGTCTCCCAGCATTGTAACAATCGCATGAAGAAATAATCTGGTTTTCTTTTTGAATGTACTATATAG
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 77.70% | 22.30% | 0.04% | 0.00% | NA |
All Indica | 2759 | 68.40% | 31.50% | 0.07% | 0.00% | NA |
All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Aus | 269 | 58.40% | 41.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 45.60% | 54.20% | 0.22% | 0.00% | NA |
Indica III | 913 | 64.30% | 35.70% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 65.80% | 34.10% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 55.20% | 44.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 77.80% | 22.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0906442847 | T -> A | LOC_Os09g11510.1 | upstream_gene_variant ; 3922.0bp to feature; MODIFIER | silent_mutation | Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
vg0906442847 | T -> A | LOC_Os09g11520.1 | upstream_gene_variant ; 942.0bp to feature; MODIFIER | silent_mutation | Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
vg0906442847 | T -> A | LOC_Os09g11550.1 | upstream_gene_variant ; 3204.0bp to feature; MODIFIER | silent_mutation | Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
vg0906442847 | T -> A | LOC_Os09g11540.1 | downstream_gene_variant ; 2013.0bp to feature; MODIFIER | silent_mutation | Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
vg0906442847 | T -> A | LOC_Os09g11530.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.601; most accessible tissue: Minghui63 panicle, score: 84.005 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0906442847 | 3.81E-06 | NA | mr1004_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 |
vg0906442847 | 5.58E-06 | 7.92E-06 | mr1004_2 | Ind_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 |