Search for Variation information by Variation ID:

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

Detailed information for vg0906778436:

Variant ID: vg0906778436 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6778436
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACTAAACTAATAAAATAATATATTGATAGTCTAAGATGGATACAACTTCATATTCACTAATTATGAATTTTGGAATTATCAGTCTTTATGCAACTAAAA[C/A]
AAATGAATCCATATATACATATAGTTTATTTCAAATGTAGAACTTATTGTTAACTGCCATTTCAGCATATAGAGAAGAACAATTAGATGATATTGATGTG

Reverse complement sequence

CACATCAATATCATCTAATTGTTCTTCTCTATATGCTGAAATGGCAGTTAACAATAAGTTCTACATTTGAAATAAACTATATGTATATATGGATTCATTT[G/T]
TTTTAGTTGCATAAAGACTGATAATTCCAAAATTCATAATTAGTGAATATGAAGTTGTATCCATCTTAGACTATCAATATATTATTTTATTAGTTTAGTC

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	96.30%	3.70%	0.02%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.04%	0.00%	NA
All Japonica	1512	89.40%	10.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.00%	0.13%	0.00%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	88.70%	11.30%	0.00%	0.00%	NA
Japonica Intermediate	241	68.00%	32.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0906778436	C -> A	LOC_Os09g12020-LOC_Os09g12050	intergenic_region ; MODIFIER	silent_mutation	Average:39.052; most accessible tissue: Callus, score: 71.703	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906778436	2.87E-06	NA	mr1540_2	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
vg0906778436	1.55E-06	NA	mr1732_2	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