Search for Variation information by Variation ID:

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

Detailed information for vg1002271984:

Variant ID: vg1002271984 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 2271984
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.28, others allele: 0.00, population size: 61. )

Flanking Sequence (100 bp) in Reference Genome:

GACGGGGACGGCGTTCCCGGGTCGAGGATCGCTGCCACCGACCCCGTTTCCTATGACTATGGGAACAACTTCATGTTTATTAATTCTGGATTTAGAGGAA[G/A]
ACAATAAGCTTTGGAAAAAAAACTAAAACCTAAAGAGTGCATGATATATTATTTATATTTTTTAGGAACTGAACTATTGGCGTTCGATTAACAGCTATAA

Reverse complement sequence

TTATAGCTGTTAATCGAACGCCAATAGTTCAGTTCCTAAAAAATATAAATAATATATCATGCACTCTTTAGGTTTTAGTTTTTTTTCCAAAGCTTATTGT[C/T]
TTCCTCTAAATCCAGAATTAATAAACATGAAGTTGTTCCCATAGTCATAGGAAACGGGGTCGGTGGCAGCGATCCTCGACCCGGGAACGCCGTCCCCGTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.00%	18.90%	0.68%	58.40%	NA
All Indica	2759	14.90%	2.60%	0.98%	81.55%	NA
All Japonica	1512	31.70%	52.80%	0.13%	15.41%	NA
Aus	269	13.80%	0.40%	0.74%	85.13%	NA
Indica I	595	31.80%	1.80%	1.18%	65.21%	NA
Indica II	465	2.60%	0.90%	1.29%	95.27%	NA
Indica III	913	14.10%	3.50%	0.55%	81.82%	NA
Indica Intermediate	786	10.30%	3.10%	1.15%	85.50%	NA
Temperate Japonica	767	41.30%	49.80%	0.00%	8.87%	NA
Tropical Japonica	504	7.10%	71.20%	0.40%	21.23%	NA
Japonica Intermediate	241	52.30%	23.70%	0.00%	24.07%	NA
VI/Aromatic	96	84.40%	9.40%	0.00%	6.25%	NA
Intermediate	90	36.70%	15.60%	1.11%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1002271984	G -> A	LOC_Os10g04740.1	upstream_gene_variant ; 748.0bp to feature; MODIFIER	silent_mutation	Average:11.752; most accessible tissue: Callus, score: 41.724	N	N	N	N
vg1002271984	G -> A	LOC_Os10g04740-LOC_Os10g04750	intergenic_region ; MODIFIER	silent_mutation	Average:11.752; most accessible tissue: Callus, score: 41.724	N	N	N	N
vg1002271984	G -> DEL	N	N	silent_mutation	Average:11.752; most accessible tissue: Callus, score: 41.724	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1002271984	NA	3.79E-07	mr1606	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
vg1002271984	NA	2.22E-09	mr1709_2	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
vg1002271984	5.73E-06	3.76E-07	mr1768_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
vg1002271984	6.95E-06	NA	mr1829_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