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Detailed information for vg0315952781:

Variant ID: vg0315952781 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15952781
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

AGGGAGAGGATGGCGGCGTGGCCATGGACTCGTAGCGGCTAGGAGCTATATTGGTTGGGGAGGAGCGCCCATAATCAGAGCCCCGGGGATGTAGGCTTCA[A/G]
CTGAAGCTTGTTAACAAATATCGTGTGTTCCTATGTCGTCATCTGGCATGTCTTGGGTGATCAATGACTGAAGCAATCAGGAGGGTTAGTCGTCTTTCCG

Reverse complement sequence

CGGAAAGACGACTAACCCTCCTGATTGCTTCAGTCATTGATCACCCAAGACATGCCAGATGACGACATAGGAACACACGATATTTGTTAACAAGCTTCAG[T/C]
TGAAGCCTACATCCCCGGGGCTCTGATTATGGGCGCTCCTCCCCAACCAATATAGCTCCTAGCCGCTACGAGTCCATGGCCACGCCGCCATCCTCTCCCT

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	26.80%	8.80%	12.10%	52.22%	NA
All Indica	2759	2.50%	9.40%	14.32%	73.79%	NA
All Japonica	1512	72.50%	4.20%	6.75%	16.53%	NA
Aus	269	1.90%	31.60%	21.56%	44.98%	NA
Indica I	595	2.00%	5.20%	10.08%	82.69%	NA
Indica II	465	3.40%	12.90%	20.00%	63.66%	NA
Indica III	913	2.30%	9.40%	12.60%	75.68%	NA
Indica Intermediate	786	2.50%	10.40%	16.16%	70.87%	NA
Temperate Japonica	767	96.00%	0.30%	1.30%	2.48%	NA
Tropical Japonica	504	36.10%	10.10%	16.27%	37.50%	NA
Japonica Intermediate	241	73.90%	4.60%	4.15%	17.43%	NA
VI/Aromatic	96	74.00%	6.20%	3.12%	16.67%	NA
Intermediate	90	30.00%	4.40%	15.56%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315952781	A -> DEL	N	N	silent_mutation	Average:62.227; most accessible tissue: Minghui63 root, score: 75.806	N	N	N	N
vg0315952781	A -> G	LOC_Os03g27810.1	downstream_gene_variant ; 1888.0bp to feature; MODIFIER	silent_mutation	Average:62.227; most accessible tissue: Minghui63 root, score: 75.806	N	N	N	N
vg0315952781	A -> G	LOC_Os03g27810-LOC_Os03g27820	intergenic_region ; MODIFIER	silent_mutation	Average:62.227; most accessible tissue: Minghui63 root, score: 75.806	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315952781	NA	1.33E-06	mr1063	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
vg0315952781	NA	1.32E-07	mr1162	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
vg0315952781	1.43E-06	1.14E-06	mr1564	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
vg0315952781	NA	3.03E-08	mr1691	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
vg0315952781	NA	3.00E-12	mr1741	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