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Detailed information for vg0819620862:

Variant ID: vg0819620862 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19620862
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTCTTAATACCTGGTCCCACCTGTCATACACACATTACGTCTTGGAGTCCATGCTGCAGCTGGCTACAGATCTATAGCCCGCTGCTCTTCTCTCTCTTT[T/C]
TTTATCTCTTTAAAATATGTTTATAGCTGGCTTATAGCCTGCTATTGTACCTGCTCTTATCCACCCACCTCTCCAGAATAAAAATATCTCCAACTCTCCT

Reverse complement sequence

AGGAGAGTTGGAGATATTTTTATTCTGGAGAGGTGGGTGGATAAGAGCAGGTACAATAGCAGGCTATAAGCCAGCTATAAACATATTTTAAAGAGATAAA[A/G]
AAAGAGAGAGAAGAGCAGCGGGCTATAGATCTGTAGCCAGCTGCAGCATGGACTCCAAGACGTAATGTGTGTATGACAGGTGGGACCAGGTATTAAGAGC

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	67.80%	32.20%	0.00%	0.00%	NA
All Indica	2759	98.00%	2.00%	0.00%	0.00%	NA
All Japonica	1512	9.20%	90.80%	0.00%	0.00%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	97.00%	3.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.70%	0.00%	0.00%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	20.80%	79.20%	0.00%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	0.00%	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
vg0819620862	T -> C	LOC_Os08g31660-LOC_Os08g31670	intergenic_region ; MODIFIER	silent_mutation	Average:52.362; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819620862	NA	1.08E-27	mr1638	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
vg0819620862	1.34E-06	NA	mr1699	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
vg0819620862	NA	4.51E-11	mr1714	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
vg0819620862	NA	8.85E-06	mr1890	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