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Detailed information for vg0609902526:

Variant ID: vg0609902526 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9902526
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.29, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GGTTGATGATCCCTGCAATGCAAACGAGAGAACACTGCAAGAACAAGATAAGATGCAATCTAAATATCGCGAATAGGTGATTAAGCACAAAGGAATAGTT[G/A]
CAATTGAAGTGGTAGATCTAATCGACCCGACAAATCAACACACCAACTATTGGGGGCTCTGAATCAATAGTCGCCGACTAATCGAGCGAGGACTAGAGAC

Reverse complement sequence

GTCTCTAGTCCTCGCTCGATTAGTCGGCGACTATTGATTCAGAGCCCCCAATAGTTGGTGTGTTGATTTGTCGGGTCGATTAGATCTACCACTTCAATTG[C/T]
AACTATTCCTTTGTGCTTAATCACCTATTCGCGATATTTAGATTGCATCTTATCTTGTTCTTGCAGTGTTCTCTCGTTTGCATTGCAGGGATCATCAACC

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	66.10%	11.70%	0.40%	21.86%	NA
All Indica	2759	97.70%	0.80%	0.00%	1.56%	NA
All Japonica	1512	22.60%	31.20%	0.93%	45.24%	NA
Aus	269	3.00%	16.40%	0.37%	80.30%	NA
Indica I	595	97.60%	0.80%	0.00%	1.51%	NA
Indica II	465	97.80%	0.00%	0.00%	2.15%	NA
Indica III	913	98.10%	1.20%	0.00%	0.66%	NA
Indica Intermediate	786	97.10%	0.60%	0.00%	2.29%	NA
Temperate Japonica	767	15.80%	57.10%	0.13%	26.99%	NA
Tropical Japonica	504	34.90%	1.80%	0.99%	62.30%	NA
Japonica Intermediate	241	18.70%	10.40%	3.32%	67.63%	NA
VI/Aromatic	96	13.50%	4.20%	3.12%	79.17%	NA
Intermediate	90	72.20%	11.10%	1.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0609902526	G -> A	LOC_Os06g17080.1	downstream_gene_variant ; 1574.0bp to feature; MODIFIER	silent_mutation	Average:55.378; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0609902526	G -> A	LOC_Os06g17070-LOC_Os06g17080	intergenic_region ; MODIFIER	silent_mutation	Average:55.378; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg0609902526	G -> DEL	N	N	silent_mutation	Average:55.378; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609902526	9.60E-09	NA	mr1768_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
vg0609902526	NA	1.10E-07	mr1768_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