Search for Variation information by Variation ID:

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

Detailed information for vg0907769964:

Variant ID: vg0907769964 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7769964
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

AAGGACCGTTTCCTTGGAATTTCATCCGAACATAAGGCAAGTGCGACCACATGGGTGGAATGGGACGCCCCTGGCTGAGTAATTAGCTAATCAAGGGAGC[C/T]
ATGATGCCAAGAGACATGTGGATTCAACGGGGTGGTGCCGGGGAGAACCCCCGGGTTTCCTGGCATAGTATGGTCCGGGACCTAACCTGGTGTTGGTTTG

Reverse complement sequence

CAAACCAACACCAGGTTAGGTCCCGGACCATACTATGCCAGGAAACCCGGGGGTTCTCCCCGGCACCACCCCGTTGAATCCACATGTCTCTTGGCATCAT[G/A]
GCTCCCTTGATTAGCTAATTACTCAGCCAGGGGCGTCCCATTCCACCCATGTGGTCGCACTTGCCTTATGTTCGGATGAAATTCCAAGGAAACGGTCCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	34.90%	1.25%	13.92%	NA
All Indica	2759	82.90%	12.00%	0.40%	4.68%	NA
All Japonica	1512	1.30%	67.10%	1.46%	30.16%	NA
Aus	269	5.60%	89.60%	3.35%	1.49%	NA
Indica I	595	89.20%	5.50%	0.17%	5.04%	NA
Indica II	465	88.80%	9.50%	0.00%	1.72%	NA
Indica III	913	79.80%	14.10%	0.77%	5.26%	NA
Indica Intermediate	786	78.20%	15.90%	0.38%	5.47%	NA
Temperate Japonica	767	0.70%	88.90%	0.39%	10.04%	NA
Tropical Japonica	504	2.00%	28.60%	3.17%	66.27%	NA
Japonica Intermediate	241	1.70%	78.40%	1.24%	18.67%	NA
VI/Aromatic	96	5.20%	21.90%	14.58%	58.33%	NA
Intermediate	90	34.40%	47.80%	3.33%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907769964	C -> DEL	N	N	silent_mutation	Average:50.631; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0907769964	C -> T	LOC_Os09g13430.1	upstream_gene_variant ; 842.0bp to feature; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0907769964	C -> T	LOC_Os09g13440.1	downstream_gene_variant ; 3063.0bp to feature; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N
vg0907769964	C -> T	LOC_Os09g13420-LOC_Os09g13430	intergenic_region ; MODIFIER	silent_mutation	Average:50.631; most accessible tissue: Zhenshan97 flag leaf, score: 70.425	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907769964	NA	3.74E-14	mr1807	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
vg0907769964	NA	3.58E-23	mr1708_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
vg0907769964	2.92E-06	2.03E-07	mr1708_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