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Detailed information for vg0920103821:

Variant ID: vg0920103821 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20103821
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGAAATCTGTTTAAAAAAACTCGCATCCTAACTTGAGACGATCGGACTGCAAAGAGGAAGATATAGGGATCGAGCTGCAAGAACACAAATCCGAGCACA[T/G]
GGAGAAGGAATGGAATGGAATGGATGGGACTGGGAACATGAGAAAAATGGGTTGTTTACCTTTGGATTCGAGTGAATTTTCACCAATTTTGGCTCTGTTT

Reverse complement sequence

AAACAGAGCCAAAATTGGTGAAAATTCACTCGAATCCAAAGGTAAACAACCCATTTTTCTCATGTTCCCAGTCCCATCCATTCCATTCCATTCCTTCTCC[A/C]
TGTGCTCGGATTTGTGTTCTTGCAGCTCGATCCCTATATCTTCCTCTTTGCAGTCCGATCGTCTCAAGTTAGGATGCGAGTTTTTTTAAACAGATTTCTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.20%	0.30%	1.48%	7.07%	NA
All Indica	2759	91.30%	0.30%	1.16%	7.25%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.07%	NA
Aus	269	39.40%	1.90%	13.38%	45.35%	NA
Indica I	595	92.90%	0.20%	2.69%	4.20%	NA
Indica II	465	93.10%	0.40%	0.65%	5.81%	NA
Indica III	913	92.10%	0.30%	0.55%	7.01%	NA
Indica Intermediate	786	88.20%	0.10%	1.02%	10.69%	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	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	88.90%	0.00%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0920103821	T -> G	LOC_Os09g34070.2	downstream_gene_variant ; 3213.0bp to feature; MODIFIER	silent_mutation	Average:42.004; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0920103821	T -> G	LOC_Os09g34060-LOC_Os09g34070	intergenic_region ; MODIFIER	silent_mutation	Average:42.004; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0920103821	T -> DEL	N	N	silent_mutation	Average:42.004; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920103821	2.82E-08	9.33E-14	mr1216	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
vg0920103821	3.89E-09	1.46E-14	mr1216	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
vg0920103821	NA	5.46E-21	mr1817	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
vg0920103821	NA	1.09E-06	mr1158_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
vg0920103821	NA	1.79E-08	mr1510_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
vg0920103821	7.87E-09	NA	mr1793_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
vg0920103821	2.69E-06	2.15E-07	mr1793_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
vg0920103821	1.78E-06	4.10E-20	mr1817_2	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