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Detailed information for vg1004761610:

Variant ID: vg1004761610 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4761610
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACATTAATCACGTCAGTGATGCTGCTAAAAAGAAAAGGAAAAACAAGCAACTTACATCAACTTACGCATGTAATTTTTGGGGTTACATATGTAATTTT[G/A]
AAACTTACGCTATAAATATATTAAAATTACATATGTAATTTTAAAACTTACAGCGTAAATATATTAAAATTACATATGTAATTTTGAAGATTTACGATGT

Reverse complement sequence

ACATCGTAAATCTTCAAAATTACATATGTAATTTTAATATATTTACGCTGTAAGTTTTAAAATTACATATGTAATTTTAATATATTTATAGCGTAAGTTT[C/T]
AAAATTACATATGTAACCCCAAAAATTACATGCGTAAGTTGATGTAAGTTGCTTGTTTTTCCTTTTCTTTTTAGCAGCATCACTGACGTGATTAATGTCC

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	89.20%	10.80%	0.02%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.04%	0.00%	NA
All Japonica	1512	80.40%	19.60%	0.00%	0.00%	NA
Aus	269	98.50%	1.50%	0.00%	0.00%	NA
Indica I	595	99.20%	0.80%	0.00%	0.00%	NA
Indica II	465	88.20%	11.80%	0.00%	0.00%	NA
Indica III	913	90.40%	9.60%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.80%	0.13%	0.00%	NA
Temperate Japonica	767	80.20%	19.80%	0.00%	0.00%	NA
Tropical Japonica	504	87.10%	12.90%	0.00%	0.00%	NA
Japonica Intermediate	241	66.80%	33.20%	0.00%	0.00%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	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
vg1004761610	G -> A	LOC_Os10g08790.1	upstream_gene_variant ; 1259.0bp to feature; MODIFIER	silent_mutation	Average:44.404; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1004761610	G -> A	LOC_Os10g08780.1	downstream_gene_variant ; 3442.0bp to feature; MODIFIER	silent_mutation	Average:44.404; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1004761610	G -> A	LOC_Os10g08800.1	downstream_gene_variant ; 2829.0bp to feature; MODIFIER	silent_mutation	Average:44.404; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg1004761610	G -> A	LOC_Os10g08780-LOC_Os10g08790	intergenic_region ; MODIFIER	silent_mutation	Average:44.404; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004761610	NA	7.15E-06	mr1002	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
vg1004761610	4.58E-06	3.41E-07	mr1708	Jap_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