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Detailed information for vg0400438884:

Variant ID: vg0400438884 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 438884
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTTTACTCTTTCATTAGTGTGATTAACCAGAAAAATAGTTTTAGTTACTAGGATATTATCAATAAAGTATATGTTATACTACTATGTCTGAGCTAAA[A/G]
CTTAGTTGAGCTCAAATTGAGCTTGCTTAAAAGTTCGTAGGTGGAATAAGCTTGGTTTGGCTTGCGCTTGCCAAGCTTGAGCTAGGAAAGGGGAGGTCTC

Reverse complement sequence

GAGACCTCCCCTTTCCTAGCTCAAGCTTGGCAAGCGCAAGCCAAACCAAGCTTATTCCACCTACGAACTTTTAAGCAAGCTCAATTTGAGCTCAACTAAG[T/C]
TTTAGCTCAGACATAGTAGTATAACATATACTTTATTGATAATATCCTAGTAACTAAAACTATTTTTCTGGTTAATCACACTAATGAAAGAGTAAAAGAA

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	67.20%	32.40%	0.32%	0.00%	NA
All Indica	2759	82.70%	16.90%	0.36%	0.00%	NA
All Japonica	1512	39.30%	60.50%	0.20%	0.00%	NA
Aus	269	79.90%	19.70%	0.37%	0.00%	NA
Indica I	595	93.80%	5.90%	0.34%	0.00%	NA
Indica II	465	87.30%	12.70%	0.00%	0.00%	NA
Indica III	913	73.90%	26.00%	0.11%	0.00%	NA
Indica Intermediate	786	81.90%	17.20%	0.89%	0.00%	NA
Temperate Japonica	767	51.80%	47.80%	0.39%	0.00%	NA
Tropical Japonica	504	24.60%	75.40%	0.00%	0.00%	NA
Japonica Intermediate	241	30.30%	69.70%	0.00%	0.00%	NA
VI/Aromatic	96	26.00%	74.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	31.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400438884	A -> G	LOC_Os04g01640.1	downstream_gene_variant ; 4883.0bp to feature; MODIFIER	silent_mutation	Average:47.642; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0400438884	A -> G	LOC_Os04g01650.1	downstream_gene_variant ; 4425.0bp to feature; MODIFIER	silent_mutation	Average:47.642; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0400438884	A -> G	LOC_Os04g01640-LOC_Os04g01650	intergenic_region ; MODIFIER	silent_mutation	Average:47.642; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400438884	6.35E-09	NA	mr1672_2	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
vg0400438884	9.10E-11	NA	mr1672_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