Variant ID: vg0333546429 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 33546429 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.07, others allele: 0.00, population size: 204. )
TTAATTATTGAATCTGTTGTTACAACTTTACACAACACCAATACTCTATACTAATCTAGCAACTGGAGTATATTTATCCACAACATTCAAGGAAACATGA[T/A]
ACTTGTATGCGTATATAGGGGTGGCGCACATGTATTTATACTGTATTTCTCGACAAAAATATTATATGTACGTACATTTCAAATTAATACGTATGAACAC
GTGTTCATACGTATTAATTTGAAATGTACGTACATATAATATTTTTGTCGAGAAATACAGTATAAATACATGTGCGCCACCCCTATATACGCATACAAGT[A/T]
TCATGTTTCCTTGAATGTTGTGGATAAATATACTCCAGTTGCTAGATTAGTATAGAGTATTGGTGTTGTGTAAAGTTGTAACAACAGATTCAATAATTAA
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 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
All Indica | 2759 | 73.10% | 26.90% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 1.50% | 98.50% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 80.40% | 19.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 54.50% | 45.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 72.00% | 28.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 83.30% | 16.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0333546429 | T -> A | LOC_Os03g58910.2 | upstream_gene_variant ; 1855.0bp to feature; MODIFIER | silent_mutation | Average:58.283; most accessible tissue: Callus, score: 87.436 | N | N | N | N |
vg0333546429 | T -> A | LOC_Os03g58920.2 | downstream_gene_variant ; 34.0bp to feature; MODIFIER | silent_mutation | Average:58.283; most accessible tissue: Callus, score: 87.436 | N | N | N | N |
vg0333546429 | T -> A | LOC_Os03g58920.1 | downstream_gene_variant ; 34.0bp to feature; MODIFIER | silent_mutation | Average:58.283; most accessible tissue: Callus, score: 87.436 | N | N | N | N |
vg0333546429 | T -> A | LOC_Os03g58910-LOC_Os03g58920 | intergenic_region ; MODIFIER | silent_mutation | Average:58.283; most accessible tissue: Callus, score: 87.436 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0333546429 | NA | 6.99E-07 | Spikelet_length | Ind_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0333546429 | NA | 3.00E-09 | mr1860_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 |