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Detailed information for vg1004572556:

Variant ID: vg1004572556 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4572556
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCCCCAGCCGTGAAGTTGGAAAGTTCATTTCCGATTACGCGGCTTGGTTAATACGCATGGGGAGAACTCTTACACGACCAGGTCTGACATGGTCTTTC[G/A]
TCTCTACAAAATCCGACAAGGCCTTATCGGCTCTGGGCGTCCCCAGCCGAAGATCCCTTAGGTTTCTCGGAGGCCTTGTCAGCATGGCGTAAAGGGACAT

Reverse complement sequence

ATGTCCCTTTACGCCATGCTGACAAGGCCTCCGAGAAACCTAAGGGATCTTCGGCTGGGGACGCCCAGAGCCGATAAGGCCTTGTCGGATTTTGTAGAGA[C/T]
GAAAGACCATGTCAGACCTGGTCGTGTAAGAGTTCTCCCCATGCGTATTAACCAAGCCGCGTAATCGGAAATGAACTTTCCAACTTCACGGCTGGGGGCT

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	67.80%	31.30%	0.47%	0.36%	NA
All Indica	2759	53.60%	45.10%	0.65%	0.62%	NA
All Japonica	1512	87.40%	12.40%	0.13%	0.00%	NA
Aus	269	95.50%	4.50%	0.00%	0.00%	NA
Indica I	595	59.30%	40.00%	0.67%	0.00%	NA
Indica II	465	40.20%	55.30%	1.72%	2.80%	NA
Indica III	913	50.90%	48.70%	0.11%	0.22%	NA
Indica Intermediate	786	60.40%	38.70%	0.64%	0.25%	NA
Temperate Japonica	767	93.40%	6.60%	0.00%	0.00%	NA
Tropical Japonica	504	86.90%	12.90%	0.20%	0.00%	NA
Japonica Intermediate	241	69.70%	29.90%	0.41%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	73.30%	24.40%	2.22%	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
vg1004572556	G -> A	LOC_Os10g08410.1	downstream_gene_variant ; 1690.0bp to feature; MODIFIER	silent_mutation	Average:49.496; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg1004572556	G -> A	LOC_Os10g08420.1	downstream_gene_variant ; 233.0bp to feature; MODIFIER	silent_mutation	Average:49.496; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg1004572556	G -> A	LOC_Os10g08410-LOC_Os10g08420	intergenic_region ; MODIFIER	silent_mutation	Average:49.496; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N
vg1004572556	G -> DEL	N	N	silent_mutation	Average:49.496; most accessible tissue: Zhenshan97 flag leaf, score: 65.3	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004572556	NA	1.01E-06	mr1053	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
vg1004572556	1.14E-06	NA	mr1853	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
vg1004572556	4.41E-07	4.41E-07	mr1853	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
vg1004572556	NA	3.93E-06	mr1053_2	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
vg1004572556	NA	3.02E-06	mr1308_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