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Detailed information for vg0820033637:

Variant ID: vg0820033637 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20033637
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGATGTCGGAAGGAGTTTTGAACACGAATGAAAAAACTATTTTCATAACTTGTCTGGAAACCGCGAGACGAACTTATTAAGCCTAGTTAATCCATCATTA[G/A]
CACATATGGGTTACTGTAGTACTTATAGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCGCGATTTCCATGCAAACTGTTAAATTAGTTTTTTT

Reverse complement sequence

AAAAAAACTAATTTAACAGTTTGCATGGAAATCGCGAGACGAATCTTTTGAGCCTAATTAGTCCATGATTAGCTATAAGTACTACAGTAACCCATATGTG[C/T]
TAATGATGGATTAACTAGGCTTAATAAGTTCGTCTCGCGGTTTCCAGACAAGTTATGAAAATAGTTTTTTCATTCGTGTTCAAAACTCCTTCCGACATCC

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	83.10%	11.90%	0.32%	4.63%	NA
All Indica	2759	73.40%	19.00%	0.51%	7.14%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.07%	NA
Aus	269	85.90%	11.90%	0.00%	2.23%	NA
Indica I	595	82.00%	18.00%	0.00%	0.00%	NA
Indica II	465	88.20%	3.20%	0.86%	7.74%	NA
Indica III	913	60.10%	27.50%	0.66%	11.72%	NA
Indica Intermediate	786	73.50%	19.10%	0.51%	6.87%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	89.60%	0.00%	0.00%	10.42%	NA
Intermediate	90	85.60%	8.90%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0820033637	G -> A	LOC_Os08g32350.1	downstream_gene_variant ; 466.0bp to feature; MODIFIER	silent_mutation	Average:19.742; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0820033637	G -> A	LOC_Os08g32350.2	intron_variant ; MODIFIER	silent_mutation	Average:19.742; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0820033637	G -> DEL	N	N	silent_mutation	Average:19.742; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820033637	NA	7.24E-07	mr1138	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
vg0820033637	3.81E-06	3.81E-06	mr1717	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
vg0820033637	NA	6.82E-07	mr1728	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
vg0820033637	NA	3.93E-06	mr1138_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
vg0820033637	NA	5.41E-06	mr1566_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
vg0820033637	7.44E-06	6.37E-09	mr1860_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
vg0820033637	NA	8.90E-06	mr1908_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
vg0820033637	NA	2.44E-06	mr1996_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
vg0820033637	NA	3.07E-06	mr1996_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