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Detailed information for vg0217766680:

Variant ID: vg0217766680 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17766680
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATCACATAAGGATTAGAAACTTTTCTCCAAATATCAAGATACTCAGGTTGAATATAAGATTGCATCTTACTACACTAATAAGGAAAATCCGTTCCATC[G/A]
AAAACATCAGGCTTAATTGCAAACTTAAGAGCCATGGCAAAAACTCAAGATCGGTAAAGATCAAGAAGAGCAAACGTGGCTCTGATACCACTTGTAGGAT

Reverse complement sequence

ATCCTACAAGTGGTATCAGAGCCACGTTTGCTCTTCTTGATCTTTACCGATCTTGAGTTTTTGCCATGGCTCTTAAGTTTGCAATTAAGCCTGATGTTTT[C/T]
GATGGAACGGATTTTCCTTATTAGTGTAGTAAGATGCAATCTTATATTCAACCTGAGTATCTTGATATTTGGAGAAAAGTTTCTAATCCTTATGTGATTC

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	35.80%	2.40%	8.55%	53.30%	NA
All Indica	2759	9.80%	0.10%	12.83%	77.27%	NA
All Japonica	1512	89.60%	7.10%	1.98%	1.39%	NA
Aus	269	2.60%	0.00%	4.46%	92.94%	NA
Indica I	595	6.90%	0.20%	12.10%	80.84%	NA
Indica II	465	14.20%	0.00%	18.49%	67.31%	NA
Indica III	913	10.00%	0.00%	9.31%	80.72%	NA
Indica Intermediate	786	9.20%	0.30%	14.12%	76.46%	NA
Temperate Japonica	767	84.20%	11.30%	3.13%	1.30%	NA
Tropical Japonica	504	98.20%	0.00%	0.60%	1.19%	NA
Japonica Intermediate	241	88.40%	8.30%	1.24%	2.07%	NA
VI/Aromatic	96	15.60%	0.00%	3.12%	81.25%	NA
Intermediate	90	48.90%	3.30%	5.56%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217766680	G -> A	LOC_Os02g29880.1	upstream_gene_variant ; 3735.0bp to feature; MODIFIER	silent_mutation	Average:24.831; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg0217766680	G -> A	LOC_Os02g29870.1	intron_variant ; MODIFIER	silent_mutation	Average:24.831; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg0217766680	G -> DEL	N	N	silent_mutation	Average:24.831; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217766680	2.12E-06	1.94E-06	mr1657	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