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Detailed information for vg0821141087:

Variant ID: vg0821141087 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21141087
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGGCGAAGGGGTAAGTTCTACGTTCCGCCAGCCTTGGTGAATCTATTAGCTAAATGGTGTTGTTCAAGGCTGCATCACTTCGATCTCTTGGATCGCTCT[A/G]
GTTTGGTTGATATATTTGCCTATCTGATATCTAAATTCTATCTCTAATTGCATTGTGTTTAGAGACGCATCGGTTTAGTCGGGACTGTCTCGGTTAGGTC

Reverse complement sequence

GACCTAACCGAGACAGTCCCGACTAAACCGATGCGTCTCTAAACACAATGCAATTAGAGATAGAATTTAGATATCAGATAGGCAAATATATCAACCAAAC[T/C]
AGAGCGATCCAAGAGATCGAAGTGATGCAGCCTTGAACAACACCATTTAGCTAATAGATTCACCAAGGCTGGCGGAACGTAGAACTTACCCCTTCGCCGG

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	71.90%	27.90%	0.13%	0.13%	NA
All Indica	2759	98.80%	0.80%	0.18%	0.18%	NA
All Japonica	1512	22.50%	77.40%	0.07%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.00%	0.17%	0.50%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	98.80%	1.00%	0.11%	0.11%	NA
Indica Intermediate	786	98.20%	1.30%	0.38%	0.13%	NA
Temperate Japonica	767	3.80%	96.10%	0.00%	0.13%	NA
Tropical Japonica	504	48.80%	51.20%	0.00%	0.00%	NA
Japonica Intermediate	241	27.00%	72.60%	0.41%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	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
vg0821141087	A -> G	LOC_Os08g33790.1	upstream_gene_variant ; 4901.0bp to feature; MODIFIER	silent_mutation	Average:45.197; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0821141087	A -> G	LOC_Os08g33790-LOC_Os08g33800	intergenic_region ; MODIFIER	silent_mutation	Average:45.197; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg0821141087	A -> DEL	N	N	silent_mutation	Average:45.197; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821141087	5.95E-06	NA	mr1301	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
vg0821141087	8.71E-13	2.08E-18	mr1410	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
vg0821141087	NA	3.52E-16	mr1410	Jap_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
vg0821141087	NA	1.76E-30	mr1980	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
vg0821141087	NA	9.48E-10	mr1980	Jap_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
vg0821141087	6.03E-11	4.83E-17	mr1410_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
vg0821141087	NA	8.35E-16	mr1410_2	Jap_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
vg0821141087	NA	1.75E-08	mr1660_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