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Detailed information for vg0919618710:

Variant ID: vg0919618710 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19618710
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGATAGAGCTCTCGGATCACCAGGACCAATTTATTTGGAAATGGGAAAGTTCAGGCATGTACTCCTCCCGCTCCGCCTACCAAGCATTGTTCCTCGGT[C/T]
GAATCCCGTTCCAATCCACGCCGATCTAGAAATCGCTGGCGCCGCCGCGCTGCCGTTACTTCAGCTGGCTGGTCGCACTCAACCGCTGCTGGACGGCGGA

Reverse complement sequence

TCCGCCGTCCAGCAGCGGTTGAGTGCGACCAGCCAGCTGAAGTAACGGCAGCGCGGCGGCGCCAGCGATTTCTAGATCGGCGTGGATTGGAACGGGATTC[G/A]
ACCGAGGAACAATGCTTGGTAGGCGGAGCGGGAGGAGTACATGCCTGAACTTTCCCATTTCCAAATAAATTGGTCCTGGTGATCCGAGAGCTCTATCTCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.90%	20.00%	4.93%	22.20%	NA
All Indica	2759	20.70%	33.90%	8.23%	37.19%	NA
All Japonica	1512	99.70%	0.00%	0.13%	0.20%	NA
Aus	269	96.70%	0.40%	0.74%	2.23%	NA
Indica I	595	8.40%	33.60%	14.45%	43.53%	NA
Indica II	465	23.40%	21.70%	4.52%	50.32%	NA
Indica III	913	21.50%	44.10%	5.70%	28.70%	NA
Indica Intermediate	786	27.50%	29.40%	8.65%	34.48%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	77.80%	10.00%	2.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0919618710	C -> DEL	N	N	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0919618710	C -> T	LOC_Os09g32930.1	upstream_gene_variant ; 1913.0bp to feature; MODIFIER	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0919618710	C -> T	LOC_Os09g32930.3	upstream_gene_variant ; 1913.0bp to feature; MODIFIER	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0919618710	C -> T	LOC_Os09g32910.1	downstream_gene_variant ; 834.0bp to feature; MODIFIER	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0919618710	C -> T	LOC_Os09g32920.1	downstream_gene_variant ; 56.0bp to feature; MODIFIER	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0919618710	C -> T	LOC_Os09g32910-LOC_Os09g32920	intergenic_region ; MODIFIER	silent_mutation	Average:49.726; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919618710	2.93E-06	3.21E-08	mr1216	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
vg0919618710	3.18E-06	9.70E-09	mr1216	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