Search for Variation information by Variation ID:

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

Detailed information for vg1004708904:

Variant ID: vg1004708904 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4708904
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TGATCCATATTTACCAAGTTGTTTGATTCTTCTGAAACTCATGTGATTGTGAAGTTTAAGTTCAATGGAGTGCGGTGTTTGTGCAGATAAATAAATTCAA[C/A]
AACACCAAGACTAAGTTTTAACAACATATATAGAAACAATATATTTCGGTTTTAAGTACCCCATGGAAGAGTTGGGGCTAGCTAGTGCCAGATAGTTGAT

Reverse complement sequence

ATCAACTATCTGGCACTAGCTAGCCCCAACTCTTCCATGGGGTACTTAAAACCGAAATATATTGTTTCTATATATGTTGTTAAAACTTAGTCTTGGTGTT[G/T]
TTGAATTTATTTATCTGCACAAACACCGCACTCCATTGAACTTAAACTTCACAATCACATGAGTTTCAGAAGAATCAAACAACTTGGTAAATATGGATCA

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	93.00%	5.40%	0.06%	1.61%	NA
All Indica	2759	96.90%	0.30%	0.11%	2.72%	NA
All Japonica	1512	85.00%	15.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	92.40%	0.30%	0.33%	6.90%	NA
Indica Intermediate	786	98.30%	0.30%	0.00%	1.40%	NA
Temperate Japonica	767	78.90%	21.10%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	76.30%	23.70%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004708904	C -> A	LOC_Os10g08680.1	upstream_gene_variant ; 231.0bp to feature; MODIFIER	silent_mutation	Average:58.233; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N
vg1004708904	C -> A	LOC_Os10g08670-LOC_Os10g08680	intergenic_region ; MODIFIER	silent_mutation	Average:58.233; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N
vg1004708904	C -> DEL	N	N	silent_mutation	Average:58.233; most accessible tissue: Zhenshan97 young leaf, score: 66.32	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004708904	3.86E-07	NA	mr1062	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
vg1004708904	NA	1.76E-07	mr1062	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
vg1004708904	1.61E-06	9.62E-08	mr1525	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
vg1004708904	9.35E-06	9.35E-06	mr1525	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