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Detailed information for vg0617988684:

Variant ID: vg0617988684 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17988684
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

CTATCCCTCTAGCCGTTATGTTGTCTGTTGACACCAGCTAGAGAAGATACCAAACCTAGTCGTTATGCTCTAGCATCGACTAGCACACAACCAAACCCTA[T/G]
CCCTCCTAACCATTTATCGTTTTCTTGTTATTTTATGGCTTTTATTGAATTTAGTTCTTCGTCTTTCTTAGTAGAGTCTATTATCTTTTGGATGGCAACC

Reverse complement sequence

GGTTGCCATCCAAAAGATAATAGACTCTACTAAGAAAGACGAAGAACTAAATTCAATAAAAGCCATAAAATAACAAGAAAACGATAAATGGTTAGGAGGG[A/C]
TAGGGTTTGGTTGTGTGCTAGTCGATGCTAGAGCATAACGACTAGGTTTGGTATCTTCTCTAGCTGGTGTCAACAGACAACATAACGGCTAGAGGGATAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.60%	19.30%	0.08%	0.00%	NA
All Indica	2759	97.90%	2.00%	0.04%	0.00%	NA
All Japonica	1512	45.00%	55.00%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	96.30%	3.70%	0.00%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	55.50%	44.30%	0.13%	0.00%	NA
Tropical Japonica	504	20.60%	79.40%	0.00%	0.00%	NA
Japonica Intermediate	241	62.20%	37.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	68.90%	28.90%	2.22%	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
vg0617988684	T -> G	LOC_Os06g30930.1	upstream_gene_variant ; 4315.0bp to feature; MODIFIER	silent_mutation	Average:53.088; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0617988684	T -> G	LOC_Os06g30920.1	downstream_gene_variant ; 3838.0bp to feature; MODIFIER	silent_mutation	Average:53.088; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg0617988684	T -> G	LOC_Os06g30920-LOC_Os06g30930	intergenic_region ; MODIFIER	silent_mutation	Average:53.088; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617988684	NA	6.48E-06	mr1071	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
vg0617988684	NA	9.70E-06	mr1140	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
vg0617988684	NA	5.78E-21	mr1518	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
vg0617988684	NA	2.57E-06	mr1518	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
vg0617988684	NA	1.82E-25	mr1676	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
vg0617988684	NA	3.73E-08	mr1676	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
vg0617988684	2.83E-06	5.98E-09	mr1707	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
vg0617988684	NA	9.20E-06	mr1707_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