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Detailed information for vg0813352775:

Variant ID: vg0813352775 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13352775
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGAACAGTGGATGGTTAATATTGATGAATTATTACAGCTGTTTTACTGCTTTCAACTACCGTCTTTAAATGCTCGCTTTATGCAAATGAACCGCTCTA[A/G]
CTATCCTTTGATTATACCCTGCATCATACCCCTATTCCGGTATGACTTGCTGAGTACGGTGGTTGTACTCAGTCTTGCTCTATTTTCCCCAAAACCCCTA

Reverse complement sequence

TAGGGGTTTTGGGGAAAATAGAGCAAGACTGAGTACAACCACCGTACTCAGCAAGTCATACCGGAATAGGGGTATGATGCAGGGTATAATCAAAGGATAG[T/C]
TAGAGCGGTTCATTTGCATAAAGCGAGCATTTAAAGACGGTAGTTGAAAGCAGTAAAACAGCTGTAATAATTCATCAATATTAACCATCCACTGTTCAAC

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	68.10%	19.80%	0.06%	12.06%	NA
All Indica	2759	98.20%	1.70%	0.00%	0.11%	NA
All Japonica	1512	11.80%	57.20%	0.13%	30.89%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	96.10%	3.90%	0.00%	0.00%	NA
Indica II	465	98.70%	1.10%	0.00%	0.22%	NA
Indica III	913	99.50%	0.40%	0.00%	0.11%	NA
Indica Intermediate	786	98.00%	1.90%	0.00%	0.13%	NA
Temperate Japonica	767	13.00%	84.70%	0.00%	2.22%	NA
Tropical Japonica	504	8.50%	26.40%	0.00%	65.08%	NA
Japonica Intermediate	241	14.50%	34.00%	0.83%	50.62%	NA
VI/Aromatic	96	14.60%	1.00%	1.04%	83.33%	NA
Intermediate	90	55.60%	22.20%	0.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813352775	A -> G	LOC_Os08g22130.1	upstream_gene_variant ; 1704.0bp to feature; MODIFIER	silent_mutation	Average:61.248; most accessible tissue: Minghui63 flag leaf, score: 81.312	N	N	N	N
vg0813352775	A -> G	LOC_Os08g22130-LOC_Os08g22149	intergenic_region ; MODIFIER	silent_mutation	Average:61.248; most accessible tissue: Minghui63 flag leaf, score: 81.312	N	N	N	N
vg0813352775	A -> DEL	N	N	silent_mutation	Average:61.248; most accessible tissue: Minghui63 flag leaf, score: 81.312	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813352775	NA	1.47E-31	mr1137	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
vg0813352775	NA	9.83E-08	mr1164	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
vg0813352775	NA	2.92E-06	mr1180	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
vg0813352775	NA	5.60E-08	mr1183	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
vg0813352775	NA	8.66E-07	mr1192	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
vg0813352775	NA	3.19E-06	mr1280	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
vg0813352775	4.06E-06	1.84E-07	mr1296	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
vg0813352775	NA	7.36E-08	mr1503	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
vg0813352775	NA	9.90E-28	mr1617	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
vg0813352775	NA	3.54E-07	mr1627	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
vg0813352775	NA	4.02E-08	mr1729	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
vg0813352775	NA	2.19E-32	mr1137_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
vg0813352775	NA	7.40E-08	mr1521_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
vg0813352775	NA	2.34E-08	mr1794_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