Variant ID: vg0500854181 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 854181 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 281. )
TGGTAATTGTTCTTTTGGGTCAACTTACTAGCAAAATTCTGCTCGATTATACTAAATTGTTCATGAATTAAACACAAATCACCATTTTCCGTCCTGAATC[T/A]
ATGGTTGGAAAGTTATCAATGTTTGGATGCTGCACAAGGCTCAAAGTTCAATGTAAACAGGACCAAAAAAAAGGATTTCTGAACATTCGTCCTTTCATTC
GAATGAAAGGACGAATGTTCAGAAATCCTTTTTTTTGGTCCTGTTTACATTGAACTTTGAGCCTTGTGCAGCATCCAAACATTGATAACTTTCCAACCAT[A/T]
GATTCAGGACGGAAAATGGTGATTTGTGTTTAATTCATGAACAATTTAGTATAATCGAGCAGAATTTTGCTAGTAAGTTGACCCAAAAGAACAATTACCA
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 | 88.60% | 11.30% | 0.08% | 0.00% | NA |
All Indica | 2759 | 89.30% | 10.60% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
Aus | 269 | 77.00% | 23.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 86.90% | 13.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 86.60% | 12.80% | 0.51% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 53.10% | 46.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 12.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0500854181 | T -> A | LOC_Os05g02480.1 | downstream_gene_variant ; 3768.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500854181 | T -> A | LOC_Os05g02500.1 | downstream_gene_variant ; 4113.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500854181 | T -> A | LOC_Os05g02500.2 | downstream_gene_variant ; 4113.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500854181 | T -> A | LOC_Os05g02500.3 | downstream_gene_variant ; 4113.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
vg0500854181 | T -> A | LOC_Os05g02490.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0500854181 | 7.32E-06 | 4.39E-08 | mr1346 | 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 |
vg0500854181 | NA | 9.21E-06 | mr1577 | 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 |
vg0500854181 | NA | 6.74E-06 | mr1346_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 |
vg0500854181 | NA | 1.35E-06 | mr1754_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 |