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Detailed information for vg1011167641:

Variant ID: vg1011167641 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11167641
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CATGGCCCTTCAGGGCCAAGCACGGGGATCGCTCATGAACCTACCACCTGCCTCGGTCTACTCCTGGGAGGACTCTTGCAGTTGAGCTCCGGGTGCCATC[G/A]
AAGCCCGAGATCCCCTGTGCTGGCTCTTCCGTAGCGGCTAGTTTTGGTCCCGCTGGCTGGCTACGGTGCTCGGCCCGGCTCAACTAATCGTCCTTTCAAG

Reverse complement sequence

CTTGAAAGGACGATTAGTTGAGCCGGGCCGAGCACCGTAGCCAGCCAGCGGGACCAAAACTAGCCGCTACGGAAGAGCCAGCACAGGGGATCTCGGGCTT[C/T]
GATGGCACCCGGAGCTCAACTGCAAGAGTCCTCCCAGGAGTAGACCGAGGCAGGTGGTAGGTTCATGAGCGATCCCCGTGCTTGGCCCTGAAGGGCCATG

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	76.70%	4.70%	7.32%	11.34%	NA
All Indica	2759	90.10%	7.70%	2.03%	0.18%	NA
All Japonica	1512	62.20%	0.30%	3.44%	34.06%	NA
Aus	269	35.70%	0.00%	64.31%	0.00%	NA
Indica I	595	99.00%	0.00%	1.01%	0.00%	NA
Indica II	465	89.90%	9.70%	0.43%	0.00%	NA
Indica III	913	88.40%	8.80%	2.63%	0.22%	NA
Indica Intermediate	786	85.50%	11.10%	3.05%	0.38%	NA
Temperate Japonica	767	92.20%	0.00%	2.09%	5.74%	NA
Tropical Japonica	504	16.70%	0.60%	2.38%	80.36%	NA
Japonica Intermediate	241	62.20%	0.40%	9.96%	27.39%	NA
VI/Aromatic	96	40.60%	0.00%	54.17%	5.21%	NA
Intermediate	90	67.80%	5.60%	14.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011167641	G -> A	LOC_Os10g21760.1	upstream_gene_variant ; 98.0bp to feature; MODIFIER	silent_mutation	Average:56.771; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1011167641	G -> A	LOC_Os10g21770.1	upstream_gene_variant ; 2907.0bp to feature; MODIFIER	silent_mutation	Average:56.771; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1011167641	G -> A	LOC_Os10g21760-LOC_Os10g21770	intergenic_region ; MODIFIER	silent_mutation	Average:56.771; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1011167641	G -> DEL	N	N	silent_mutation	Average:56.771; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011167641	4.63E-06	3.70E-08	mr1672	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
vg1011167641	NA	5.04E-06	mr1672_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