Search for Variation information by Variation ID:

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

Detailed information for vg0506871793:

Variant ID: vg0506871793 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6871793
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATATAGTGCATATTATTTATTTATTTAGAATTTTTTATGGGGAAGGGGGATAGTTACAAAGTATGTACGTGCATGCGTACATATATGGGAGCAATCGAC[G/A]
TAGATGTTCTAATGATAAATTAAATCTATTTGTTATTTTTAGATCTAACGGTTAAAAATATGGTGTCCACTACATTAAGTGAAAATTAATAGCTAGATAT

Reverse complement sequence

ATATCTAGCTATTAATTTTCACTTAATGTAGTGGACACCATATTTTTAACCGTTAGATCTAAAAATAACAAATAGATTTAATTTATCATTAGAACATCTA[C/T]
GTCGATTGCTCCCATATATGTACGCATGCACGTACATACTTTGTAACTATCCCCCTTCCCCATAAAAAATTCTAAATAAATAAATAATATGCACTATATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.30%	10.70%	0.02%	0.00%	NA
All Indica	2759	82.10%	17.90%	0.04%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.60%	5.20%	0.17%	0.00%	NA
Indica II	465	70.80%	29.20%	0.00%	0.00%	NA
Indica III	913	74.50%	25.50%	0.00%	0.00%	NA
Indica Intermediate	786	88.20%	11.80%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	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	92.20%	7.80%	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
vg0506871793	G -> A	LOC_Os05g12020.1	upstream_gene_variant ; 2034.0bp to feature; MODIFIER	silent_mutation	Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0506871793	G -> A	LOC_Os05g12010.1	downstream_gene_variant ; 3552.0bp to feature; MODIFIER	silent_mutation	Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0506871793	G -> A	LOC_Os05g12010-LOC_Os05g12020	intergenic_region ; MODIFIER	silent_mutation	Average:35.132; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506871793	2.72E-70	1.58E-118	mr1039	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
vg0506871793	1.38E-54	3.55E-87	mr1039	Ind_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
vg0506871793	2.91E-27	1.45E-43	mr1632	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
vg0506871793	5.91E-23	6.60E-31	mr1632	Ind_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
vg0506871793	2.92E-85	2.03E-127	mr1039_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
vg0506871793	9.89E-62	5.65E-91	mr1039_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
vg0506871793	1.15E-11	1.07E-18	mr1514_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
vg0506871793	3.40E-10	1.59E-10	mr1514_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
vg0506871793	4.83E-45	1.44E-67	mr1632_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
vg0506871793	6.38E-35	3.72E-49	mr1632_2	Ind_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
vg0506871793	4.22E-09	NA	mr1873_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
vg0506871793	8.14E-08	1.26E-09	mr1873_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