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Detailed information for vg0909866383:

Variant ID: vg0909866383 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9866383
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

ATCATAGAGTAGCGGACAGAAAAGTTCGAATCAGATGAGCATCGTACCCTTTTCAAATCAACGGTGAGATGTCAGTGGTACCTCGAGGTACCTGGTACCT[G/A]
GTGGTACTTCCTCAAGGATGGTAAAAAATGCTCTTGGACAAAAGGGAATTTTGAAATAGTCAAGTGATTTGATCATGCTTATTTGAGTTTCATGTAATAC

Reverse complement sequence

GTATTACATGAAACTCAAATAAGCATGATCAAATCACTTGACTATTTCAAAATTCCCTTTTGTCCAAGAGCATTTTTTACCATCCTTGAGGAAGTACCAC[C/T]
AGGTACCAGGTACCTCGAGGTACCACTGACATCTCACCGTTGATTTGAAAAGGGTACGATGCTCATCTGATTCGAACTTTTCTGTCCGCTACTCTATGAT

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	38.20%	22.50%	1.38%	37.98%	NA
All Indica	2759	23.80%	21.60%	1.67%	52.95%	NA
All Japonica	1512	58.40%	27.50%	0.13%	13.96%	NA
Aus	269	75.10%	1.50%	2.97%	20.45%	NA
Indica I	595	9.90%	16.00%	2.69%	71.43%	NA
Indica II	465	15.30%	19.80%	1.72%	63.23%	NA
Indica III	913	39.30%	26.00%	0.66%	34.06%	NA
Indica Intermediate	786	21.20%	21.90%	2.04%	54.83%	NA
Temperate Japonica	767	80.20%	2.30%	0.13%	17.34%	NA
Tropical Japonica	504	16.50%	71.20%	0.00%	12.30%	NA
Japonica Intermediate	241	76.80%	16.20%	0.41%	6.64%	NA
VI/Aromatic	96	35.40%	19.80%	5.21%	39.58%	NA
Intermediate	90	33.30%	28.90%	4.44%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909866383	G -> DEL	N	N	silent_mutation	Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0909866383	G -> A	LOC_Os09g16170.1	upstream_gene_variant ; 3516.0bp to feature; MODIFIER	silent_mutation	Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0909866383	G -> A	LOC_Os09g16180.1	downstream_gene_variant ; 1146.0bp to feature; MODIFIER	silent_mutation	Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0909866383	G -> A	LOC_Os09g16180-LOC_Os09g16190	intergenic_region ; MODIFIER	silent_mutation	Average:24.296; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909866383	5.40E-07	5.40E-07	mr1260	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
vg0909866383	NA	8.19E-06	mr1505	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
vg0909866383	NA	2.14E-07	mr1807	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