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Detailed information for vg1001679807:

Variant ID: vg1001679807 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1679807
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

TCACACGAGTTTTAGCATATGTCACATAACCATGAGTATTTTAGTCCTAAGATTTCACGAAACCACAATGTTAACCAATCTATCTTAGTAGCAAAATAAA[A/G]
AATAATTCACTTACATTACTACAACATTTAATAACCCTACATCCTATTGGCCGAAGCTGGTATTGCTCTTATTCACCATAATCACACCAGTATAATATTT

Reverse complement sequence

AAATATTATACTGGTGTGATTATGGTGAATAAGAGCAATACCAGCTTCGGCCAATAGGATGTAGGGTTATTAAATGTTGTAGTAATGTAAGTGAATTATT[T/C]
TTTATTTTGCTACTAAGATAGATTGGTTAACATTGTGGTTTCGTGAAATCTTAGGACTAAAATACTCATGGTTATGTGACATATGCTAAAACTCGTGTGA

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	75.60%	18.00%	4.40%	1.97%	NA
All Indica	2759	61.80%	30.50%	7.07%	0.65%	NA
All Japonica	1512	99.50%	0.20%	0.26%	0.00%	NA
Aus	269	69.50%	0.70%	2.60%	27.14%	NA
Indica I	595	48.20%	38.20%	12.94%	0.67%	NA
Indica II	465	71.80%	20.20%	7.96%	0.00%	NA
Indica III	913	67.60%	30.60%	1.42%	0.44%	NA
Indica Intermediate	786	59.30%	30.80%	8.65%	1.27%	NA
Temperate Japonica	767	99.50%	0.30%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	6.70%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001679807	A -> G	LOC_Os10g03710.1	downstream_gene_variant ; 4617.0bp to feature; MODIFIER	silent_mutation	Average:42.859; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1001679807	A -> G	LOC_Os10g03720.1	downstream_gene_variant ; 1327.0bp to feature; MODIFIER	silent_mutation	Average:42.859; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1001679807	A -> G	LOC_Os10g03730.1	downstream_gene_variant ; 1273.0bp to feature; MODIFIER	silent_mutation	Average:42.859; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1001679807	A -> G	LOC_Os10g03720-LOC_Os10g03730	intergenic_region ; MODIFIER	silent_mutation	Average:42.859; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg1001679807	A -> DEL	N	N	silent_mutation	Average:42.859; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001679807	NA	6.16E-08	mr1136_2	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