Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0124141412:

Variant ID: vg0124141412 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24141412
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, G: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGTTCAACCAATTTCTAAGAAACAAGCCATAATCAAAATGTTCTGGTTCTACAATTTTCCTACTGATAGCCGTGTTTACTTTTGTGTGCTTACACCCT[T/G]
TTCTGCTATTTAACAGGACAGAAGCAAATGGTTCAAGATTGTGAGTAATCATTTTTCCTACATTGTCTCTTCTCTCTTGCGTATATACTATGATTGTACA

Reverse complement sequence

TGTACAATCATAGTATATACGCAAGAGAGAAGAGACAATGTAGGAAAAATGATTACTCACAATCTTGAACCATTTGCTTCTGTCCTGTTAAATAGCAGAA[A/C]
AGGGTGTAAGCACACAAAAGTAAACACGGCTATCAGTAGGAAAATTGTAGAACCAGAACATTTTGATTATGGCTTGTTTCTTAGAAATTGGTTGAACCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.60%	21.30%	0.04%	0.00%	NA
All Indica	2759	66.40%	33.50%	0.07%	0.00%	NA
All Japonica	1512	95.30%	4.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	74.80%	25.00%	0.17%	0.00%	NA
Indica II	465	63.90%	36.10%	0.00%	0.00%	NA
Indica III	913	62.40%	37.50%	0.11%	0.00%	NA
Indica Intermediate	786	66.30%	33.70%	0.00%	0.00%	NA
Temperate Japonica	767	91.00%	9.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0124141412	T -> G	LOC_Os01g42470.1	upstream_gene_variant ; 4431.0bp to feature; MODIFIER	silent_mutation	Average:42.287; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0124141412	T -> G	LOC_Os01g42470.2	upstream_gene_variant ; 4431.0bp to feature; MODIFIER	silent_mutation	Average:42.287; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0124141412	T -> G	LOC_Os01g42460.1	intron_variant ; MODIFIER	silent_mutation	Average:42.287; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124141412	5.70E-06	5.70E-06	mr1065	Jap_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
vg0124141412	7.82E-09	7.82E-09	mr1067	Jap_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
vg0124141412	4.97E-07	9.96E-07	mr1069	Jap_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
vg0124141412	2.89E-06	NA	mr1075	Jap_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
vg0124141412	5.46E-07	NA	mr1090	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
vg0124141412	7.20E-06	NA	mr1090	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
vg0124141412	2.72E-07	1.95E-06	mr1124	Jap_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
vg0124141412	3.97E-06	1.72E-06	mr1150	Jap_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
vg0124141412	1.23E-07	NA	mr1200	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
vg0124141412	5.22E-07	5.23E-07	mr1200	Jap_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
vg0124141412	1.37E-06	NA	mr1211	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
vg0124141412	3.54E-09	3.54E-09	mr1855	Jap_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
vg0124141412	2.04E-07	2.04E-07	mr1861	Jap_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