Search for Variation information by Variation ID:

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

Detailed information for vg1019343613:

Variant ID: vg1019343613 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 19343613
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

TCTATTAAGGAAATTTATTTCTTTTTTTCCACCAAAAATATTTCACCTAATGTTTCACTATATATAGATCTAATGTTGCAGTGAACTAAAACATTCCATT[G/A]
CAACAAAAAAACCCACATATTTTGGAAACCCCTTTATTAAGGGAATTCGTTTCATTTTTTGTTCCACCGAAAAATGTTTCACCTAGTGTACTTATAATGT

Reverse complement sequence

ACATTATAAGTACACTAGGTGAAACATTTTTCGGTGGAACAAAAAATGAAACGAATTCCCTTAATAAAGGGGTTTCCAAAATATGTGGGTTTTTTTGTTG[C/T]
AATGGAATGTTTTAGTTCACTGCAACATTAGATCTATATATAGTGAAACATTAGGTGAAATATTTTTGGTGGAAAAAAAGAAATAAATTTCCTTAATAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.70%	3.70%	12.72%	28.95%	NA
All Indica	2759	38.20%	5.70%	13.77%	42.33%	NA
All Japonica	1512	95.00%	0.10%	1.65%	3.31%	NA
Aus	269	7.10%	3.00%	54.28%	35.69%	NA
Indica I	595	72.10%	0.00%	4.03%	23.87%	NA
Indica II	465	16.80%	22.40%	21.51%	39.35%	NA
Indica III	913	26.30%	0.50%	13.58%	59.58%	NA
Indica Intermediate	786	39.10%	6.10%	16.79%	38.04%	NA
Temperate Japonica	767	97.90%	0.10%	1.56%	0.39%	NA
Tropical Japonica	504	91.30%	0.00%	0.60%	8.13%	NA
Japonica Intermediate	241	93.40%	0.00%	4.15%	2.49%	NA
VI/Aromatic	96	32.30%	0.00%	39.58%	28.12%	NA
Intermediate	90	48.90%	7.80%	13.33%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1019343613	G -> A	LOC_Os10g36180.1	upstream_gene_variant ; 2721.0bp to feature; MODIFIER	silent_mutation	Average:22.954; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1019343613	G -> A	LOC_Os10g36170-LOC_Os10g36180	intergenic_region ; MODIFIER	silent_mutation	Average:22.954; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1019343613	G -> DEL	N	N	silent_mutation	Average:22.954; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1019343613	NA	6.22E-06	mr1036	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
vg1019343613	NA	6.85E-07	mr1180	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
vg1019343613	NA	6.07E-13	mr1232	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
vg1019343613	NA	2.01E-07	mr1262	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
vg1019343613	NA	5.66E-07	mr1319	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
vg1019343613	NA	5.87E-06	mr1373	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
vg1019343613	NA	1.31E-06	mr1415	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
vg1019343613	NA	4.53E-19	mr1557	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
vg1019343613	NA	1.31E-06	mr1567	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
vg1019343613	NA	4.45E-07	mr1633	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
vg1019343613	NA	3.99E-09	mr1659	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
vg1019343613	NA	1.30E-07	mr1735	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
vg1019343613	NA	8.62E-06	mr1906	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
vg1019343613	NA	8.00E-12	mr1921	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