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Detailed information for vg0322577513:

Variant ID: vg0322577513 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22577513
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGAAGAAAAAAAGGAAAAAGAAAATTTTTAAAACGGTCCCATTTGTCAGTCAAAATTATGCCACGTCATATCCGTGGGACATGCCATATCAGCGCCAC[A/G]
TAGGATCCTGAAGGGGCTGTGGTGATTTCGGACCTAGATGACACACTATGACAAGTTCTGGGACTTGGATATGCATTTTGAGAGTTTAAGGATCTAGATG

Reverse complement sequence

CATCTAGATCCTTAAACTCTCAAAATGCATATCCAAGTCCCAGAACTTGTCATAGTGTGTCATCTAGGTCCGAAATCACCACAGCCCCTTCAGGATCCTA[T/C]
GTGGCGCTGATATGGCATGTCCCACGGATATGACGTGGCATAATTTTGACTGACAAATGGGACCGTTTTAAAAATTTTCTTTTTCCTTTTTTTCTTCTCT

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	89.40%	9.00%	1.67%	0.00%	NA
All Indica	2759	99.60%	0.30%	0.07%	0.00%	NA
All Japonica	1512	68.30%	26.80%	4.89%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	49.30%	42.90%	7.82%	0.00%	NA
Tropical Japonica	504	96.40%	1.80%	1.79%	0.00%	NA
Japonica Intermediate	241	70.10%	27.80%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0322577513	A -> G	LOC_Os03g40610.1	upstream_gene_variant ; 3505.0bp to feature; MODIFIER	silent_mutation	Average:36.168; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N
vg0322577513	A -> G	LOC_Os03g40610-LOC_Os03g40630	intergenic_region ; MODIFIER	silent_mutation	Average:36.168; most accessible tissue: Zhenshan97 young leaf, score: 61.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322577513	8.38E-07	NA	mr1588_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
vg0322577513	NA	5.76E-07	mr1588_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