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Detailed information for vg0321930073:

Variant ID: vg0321930073 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 21930073
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGTGGCTTGTTGAGTATGTCATATGCTCACCTTGCAATAATCAATCAACCTCAGTTGAAGAAAAAGGATCCGAAGGAGAAGACATTTGGCTTATACCC[C/A]
AGTTGAGCTGCCTGTGGGAGTGGAGCTGAAGCCATCGCTAGACCGTTATTCCGCTGCTGTTTTTCTTTTGGTTTGTAAGTATGTAACGTTATTATTATGA

Reverse complement sequence

TCATAATAATAACGTTACATACTTACAAACCAAAAGAAAAACAGCAGCGGAATAACGGTCTAGCGATGGCTTCAGCTCCACTCCCACAGGCAGCTCAACT[G/T]
GGGTATAAGCCAAATGTCTTCTCCTTCGGATCCTTTTTCTTCAACTGAGGTTGATTGATTATTGCAAGGTGAGCATATGACATACTCAACAAGCCACACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.00%	6.10%	24.65%	34.26%	NA
All Indica	2759	9.90%	0.30%	35.99%	53.86%	NA
All Japonica	1512	74.70%	18.20%	5.89%	1.19%	NA
Aus	269	40.10%	0.00%	27.14%	32.71%	NA
Indica I	595	9.20%	0.00%	36.64%	54.12%	NA
Indica II	465	5.20%	1.30%	30.11%	63.44%	NA
Indica III	913	9.00%	0.00%	42.39%	48.63%	NA
Indica Intermediate	786	14.10%	0.30%	31.55%	54.07%	NA
Temperate Japonica	767	61.90%	28.30%	9.65%	0.13%	NA
Tropical Japonica	504	93.70%	1.40%	1.59%	3.37%	NA
Japonica Intermediate	241	75.90%	21.20%	2.90%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	55.60%	6.70%	8.89%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0321930073	C -> A	LOC_Os03g39460.1	upstream_gene_variant ; 1598.0bp to feature; MODIFIER	silent_mutation	Average:9.821; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0321930073	C -> A	LOC_Os03g39490.1	upstream_gene_variant ; 3642.0bp to feature; MODIFIER	silent_mutation	Average:9.821; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0321930073	C -> A	LOC_Os03g39450.1	downstream_gene_variant ; 3116.0bp to feature; MODIFIER	silent_mutation	Average:9.821; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0321930073	C -> A	LOC_Os03g39460-LOC_Os03g39490	intergenic_region ; MODIFIER	silent_mutation	Average:9.821; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0321930073	C -> DEL	N	N	silent_mutation	Average:9.821; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0321930073	NA	1.87E-07	mr1567_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
vg0321930073	3.79E-06	NA	mr1806_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