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Detailed information for vg0608711440:

Variant ID: vg0608711440 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8711440
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCACTAGCCTCCTCCTCCTCGTTCCCCTCTACATCCCTCTCCACGTTCTCCTCCTGGTTCCCCTCCGCATCCCTCTCCACGTTCCCTTCCTCGTTCAT[G/A]
TACTGGTTTGGATCCTCGTTCCCCTCTTCTTCGTTCCAGTACTAGCTGCTTCCCTCCGCAATTGTATCGTACAGTATCTGTTCCTCATTGCGATCAGCCA

Reverse complement sequence

TGGCTGATCGCAATGAGGAACAGATACTGTACGATACAATTGCGGAGGGAAGCAGCTAGTACTGGAACGAAGAAGAGGGGAACGAGGATCCAAACCAGTA[C/T]
ATGAACGAGGAAGGGAACGTGGAGAGGGATGCGGAGGGGAACCAGGAGGAGAACGTGGAGAGGGATGTAGAGGGGAACGAGGAGGAGGAGGCTAGTGGAA

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	46.10%	1.20%	30.26%	22.47%	NA
All Indica	2759	10.90%	2.00%	49.44%	37.66%	NA
All Japonica	1512	99.00%	0.10%	0.46%	0.46%	NA
Aus	269	85.90%	0.00%	13.01%	1.12%	NA
Indica I	595	5.40%	1.20%	43.53%	49.92%	NA
Indica II	465	10.50%	1.50%	46.45%	41.51%	NA
Indica III	913	13.80%	3.40%	54.33%	28.48%	NA
Indica Intermediate	786	11.80%	1.40%	50.00%	36.77%	NA
Temperate Japonica	767	99.10%	0.00%	0.52%	0.39%	NA
Tropical Japonica	504	99.20%	0.20%	0.60%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	61.10%	0.00%	24.44%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608711440	G -> A	LOC_Os06g15340.1	upstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:17.961; most accessible tissue: Callus, score: 35.103	N	N	N	N
vg0608711440	G -> A	LOC_Os06g15330.1	downstream_gene_variant ; 4491.0bp to feature; MODIFIER	silent_mutation	Average:17.961; most accessible tissue: Callus, score: 35.103	N	N	N	N
vg0608711440	G -> A	LOC_Os06g15350.1	downstream_gene_variant ; 2809.0bp to feature; MODIFIER	silent_mutation	Average:17.961; most accessible tissue: Callus, score: 35.103	N	N	N	N
vg0608711440	G -> A	LOC_Os06g15340-LOC_Os06g15350	intergenic_region ; MODIFIER	silent_mutation	Average:17.961; most accessible tissue: Callus, score: 35.103	N	N	N	N
vg0608711440	G -> DEL	N	N	silent_mutation	Average:17.961; most accessible tissue: Callus, score: 35.103	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608711440	6.82E-06	6.81E-06	mr1048	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
vg0608711440	NA	6.16E-07	mr1570	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
vg0608711440	6.23E-07	6.23E-07	mr1663	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
vg0608711440	NA	6.52E-06	mr1920	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
vg0608711440	NA	9.77E-08	mr1570_2	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