Search for Variation information by Variation ID:

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

Detailed information for vg1122458810:

Variant ID: vg1122458810 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 22458810
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.52, G: 0.45, T: 0.02, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAAGTTTCTTAATAAAACGAATGGTCAAACATATGTTCAAAACAGAAGTCGCATCGTGTGTAGCTTGGTTTCTTTTTACTTGTTTTCGTTTCTGTTTT[A/G]
TGTAAAAGGCTCAGTTTTTAGCTTTCTCAAAAAAAAGCAGGGTAATGAAAAGTTGTGCATCAAACATAAAACCGGATTGAAAACTATTTTGCACCATATT

Reverse complement sequence

AATATGGTGCAAAATAGTTTTCAATCCGGTTTTATGTTTGATGCACAACTTTTCATTACCCTGCTTTTTTTTGAGAAAGCTAAAAACTGAGCCTTTTACA[T/C]
AAAACAGAAACGAAAACAAGTAAAAAGAAACCAAGCTACACACGATGCGACTTCTGTTTTGAACATATGTTTGACCATTCGTTTTATTAAGAAACTTAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.50%	38.40%	0.15%	0.00%	NA
All Indica	2759	58.90%	40.80%	0.22%	0.00%	NA
All Japonica	1512	78.30%	21.70%	0.00%	0.00%	NA
Aus	269	15.60%	84.40%	0.00%	0.00%	NA
Indica I	595	81.20%	18.50%	0.34%	0.00%	NA
Indica II	465	52.90%	46.90%	0.22%	0.00%	NA
Indica III	913	47.50%	52.40%	0.11%	0.00%	NA
Indica Intermediate	786	58.90%	40.80%	0.25%	0.00%	NA
Temperate Japonica	767	83.60%	16.40%	0.00%	0.00%	NA
Tropical Japonica	504	79.80%	20.20%	0.00%	0.00%	NA
Japonica Intermediate	241	58.50%	41.50%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	48.90%	50.00%	1.11%	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
vg1122458810	A -> G	LOC_Os11g37880.1	downstream_gene_variant ; 244.0bp to feature; MODIFIER	silent_mutation	Average:50.815; most accessible tissue: Callus, score: 77.686	N	N	N	N
vg1122458810	A -> G	LOC_Os11g37890.1	downstream_gene_variant ; 990.0bp to feature; MODIFIER	silent_mutation	Average:50.815; most accessible tissue: Callus, score: 77.686	N	N	N	N
vg1122458810	A -> G	LOC_Os11g37890.3	downstream_gene_variant ; 990.0bp to feature; MODIFIER	silent_mutation	Average:50.815; most accessible tissue: Callus, score: 77.686	N	N	N	N
vg1122458810	A -> G	LOC_Os11g37890.2	downstream_gene_variant ; 2235.0bp to feature; MODIFIER	silent_mutation	Average:50.815; most accessible tissue: Callus, score: 77.686	N	N	N	N
vg1122458810	A -> G	LOC_Os11g37880-LOC_Os11g37890	intergenic_region ; MODIFIER	silent_mutation	Average:50.815; most accessible tissue: Callus, score: 77.686	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1122458810	3.40E-06	3.57E-12	mr1170	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
vg1122458810	7.32E-06	1.35E-09	mr1170	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
vg1122458810	NA	7.56E-08	mr1280	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
vg1122458810	NA	7.03E-07	mr1705	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
vg1122458810	NA	3.54E-06	mr1788	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
vg1122458810	NA	9.75E-06	mr1807	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
vg1122458810	NA	5.24E-09	mr1170_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