Search for Variation information by Variation ID:

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

Detailed information for vg1121697590:

Variant ID: vg1121697590 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21697590
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTAAAACTTTTATTTTGGTCATTTCTTCATACGACAAAGTGATAGTAACATTATTCATAAAATTGACATATCTCTTATCTGGTTTTATAAACTATAACA[C/A]
ATATATGTAAAATTTATGAATAATATTACTAACATTTCGTTGGATGAAGAAATAACAAAAATAAAAGTTTTAGATCTTGATGAATTATTCAACTTTGTTG

Reverse complement sequence

CAACAAAGTTGAATAATTCATCAAGATCTAAAACTTTTATTTTTGTTATTTCTTCATCCAACGAAATGTTAGTAATATTATTCATAAATTTTACATATAT[G/T]
TGTTATAGTTTATAAAACCAGATAAGAGATATGTCAATTTTATGAATAATGTTACTATCACTTTGTCGTATGAAGAAATGACCAAAATAAAAGTTTTAGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.90%	4.70%	2.48%	0.00%	NA
All Indica	2759	92.80%	4.30%	2.86%	0.00%	NA
All Japonica	1512	98.30%	1.20%	0.53%	0.00%	NA
Aus	269	59.50%	29.70%	10.78%	0.00%	NA
Indica I	595	70.30%	17.80%	11.93%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	98.10%	1.00%	0.89%	0.00%	NA
Temperate Japonica	767	96.70%	2.20%	1.04%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1121697590	C -> A	LOC_Os11g36740-LOC_Os11g36760	intergenic_region ; MODIFIER	silent_mutation	Average:10.969; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121697590	NA	7.31E-06	mr1042_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
vg1121697590	NA	3.44E-06	mr1291_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
vg1121697590	NA	2.55E-06	mr1479_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
vg1121697590	NA	4.68E-07	mr1502_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
vg1121697590	NA	3.02E-06	mr1742_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