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Detailed information for vg0217682883:

Variant ID: vg0217682883 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17682883
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAATCAGAAGAGAAGAGTTCAACGGATGAGGAACAGGGAGCGTTTTTAGGAGGTACAACAAGAAATTAACCATCGGCTGAAGAAGACAAAGACCAAGCA[A/G]
GAGTGGCGTGTTAAGAGCACGGTCACAACAGCCGATGAAGTTGAAGCCGACAAGACCAAAAGATTGCTCAAGGGTAAGGCTACTGCATCTGCATCGGTGA

Reverse complement sequence

TCACCGATGCAGATGCAGTAGCCTTACCCTTGAGCAATCTTTTGGTCTTGTCGGCTTCAACTTCATCGGCTGTTGTGACCGTGCTCTTAACACGCCACTC[T/C]
TGCTTGGTCTTTGTCTTCTTCAGCCGATGGTTAATTTCTTGTTGTACCTCCTAAAAACGCTCCCTGTTCCTCATCCGTTGAACTCTTCTCTTCTGATTCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.80%	10.10%	10.96%	26.17%	NA
All Indica	2759	28.40%	16.50%	16.89%	38.24%	NA
All Japonica	1512	98.60%	0.10%	0.13%	1.19%	NA
Aus	269	48.70%	4.10%	12.27%	34.94%	NA
Indica I	595	46.60%	25.50%	14.29%	13.61%	NA
Indica II	465	28.80%	22.80%	17.20%	31.18%	NA
Indica III	913	18.00%	7.80%	14.90%	59.36%	NA
Indica Intermediate	786	26.50%	16.00%	20.99%	36.51%	NA
Temperate Japonica	767	98.80%	0.00%	0.26%	0.91%	NA
Tropical Japonica	504	98.40%	0.00%	0.00%	1.59%	NA
Japonica Intermediate	241	98.30%	0.40%	0.00%	1.24%	NA
VI/Aromatic	96	31.20%	6.20%	6.25%	56.25%	NA
Intermediate	90	67.80%	2.20%	12.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217682883	A -> G	LOC_Os02g29720.1	upstream_gene_variant ; 4659.0bp to feature; MODIFIER	silent_mutation	Average:33.228; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0217682883	A -> G	LOC_Os02g29730.1	intron_variant ; MODIFIER	silent_mutation	Average:33.228; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N
vg0217682883	A -> DEL	N	N	silent_mutation	Average:33.228; most accessible tissue: Minghui63 flag leaf, score: 56.489	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217682883	NA	9.85E-06	mr1231	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
vg0217682883	4.10E-06	4.10E-06	mr1762	Ind_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