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Detailed information for vg0103116049:

Variant ID: vg0103116049 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3116049
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACGCCCTGAAGTACCCCTCCCTTGCTCTAAATTCATAAAATAAATCGTCCGAAGAAATTGTTTAATTTAACCTAGAGAGAAACCCTAAATTAATAAAT[A/G]
CAAATAATAATCGGAATCGGCATGTGGAATTTTTTCTTGGGTTCTACATGTCAAAATACGCTAACAGGATTTTTAGTGGAATTTTCAGAGCCTTGGAAAT

Reverse complement sequence

ATTTCCAAGGCTCTGAAAATTCCACTAAAAATCCTGTTAGCGTATTTTGACATGTAGAACCCAAGAAAAAATTCCACATGCCGATTCCGATTATTATTTG[T/C]
ATTTATTAATTTAGGGTTTCTCTCTAGGTTAAATTAAACAATTTCTTCGGACGATTTATTTTATGAATTTAGAGCAAGGGAGGGGTACTTCAGGGCGTGA

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	62.30%	17.90%	13.27%	6.50%	NA
All Indica	2759	83.50%	2.30%	10.95%	3.30%	NA
All Japonica	1512	30.40%	43.80%	17.20%	8.66%	NA
Aus	269	44.60%	10.40%	17.10%	27.88%	NA
Indica I	595	88.70%	0.20%	8.57%	2.52%	NA
Indica II	465	72.70%	2.80%	18.28%	6.24%	NA
Indica III	913	86.90%	4.30%	6.68%	2.19%	NA
Indica Intermediate	786	81.90%	1.30%	13.36%	3.44%	NA
Temperate Japonica	767	7.40%	72.60%	8.60%	11.34%	NA
Tropical Japonica	504	65.90%	3.20%	25.60%	5.36%	NA
Japonica Intermediate	241	29.00%	36.90%	26.97%	7.05%	NA
VI/Aromatic	96	9.40%	81.20%	6.25%	3.12%	NA
Intermediate	90	60.00%	17.80%	14.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103116049	A -> G	LOC_Os01g06600.1	upstream_gene_variant ; 2086.0bp to feature; MODIFIER	silent_mutation	Average:12.566; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N
vg0103116049	A -> G	LOC_Os01g06600.2	upstream_gene_variant ; 2086.0bp to feature; MODIFIER	silent_mutation	Average:12.566; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N
vg0103116049	A -> G	LOC_Os01g06610.1	downstream_gene_variant ; 113.0bp to feature; MODIFIER	silent_mutation	Average:12.566; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N
vg0103116049	A -> G	LOC_Os01g06600-LOC_Os01g06610	intergenic_region ; MODIFIER	silent_mutation	Average:12.566; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N
vg0103116049	A -> DEL	N	N	silent_mutation	Average:12.566; most accessible tissue: Zhenshan97 flag leaf, score: 20.297	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103116049	3.59E-08	NA	mr1758_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