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Detailed information for vg0807648774:

Variant ID: vg0807648774 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7648774
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAGTTCATCTGTGACGGGCTCTAGTTTAGGCCCGATTGAGATCAGTAGTCATCTGTAACGGGCTCTAGTTTAGGCCCGATTGAGGTCAGTAGTCATCTG[T/C]
GATGGGCTCTAGTTTAGGCCCGATTGAGGTCAGTAGTCATCTGTGACGGGCTATAGTTTAGGCCCGATTGAGATGTGTATCATCTGTGATGGGCTCTAGT

Reverse complement sequence

ACTAGAGCCCATCACAGATGATACACATCTCAATCGGGCCTAAACTATAGCCCGTCACAGATGACTACTGACCTCAATCGGGCCTAAACTAGAGCCCATC[A/G]
CAGATGACTACTGACCTCAATCGGGCCTAAACTAGAGCCCGTTACAGATGACTACTGATCTCAATCGGGCCTAAACTAGAGCCCGTCACAGATGAACTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.00%	1.90%	2.01%	0.06%	NA
All Indica	2759	93.40%	3.20%	3.37%	0.11%	NA
All Japonica	1512	99.80%	0.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.00%	1.70%	2.35%	0.00%	NA
Indica II	465	93.80%	2.80%	3.23%	0.22%	NA
Indica III	913	92.70%	3.50%	3.72%	0.11%	NA
Indica Intermediate	786	92.00%	4.10%	3.82%	0.13%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0807648774	T -> C	LOC_Os08g12890.1	upstream_gene_variant ; 3809.0bp to feature; MODIFIER	silent_mutation	Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0807648774	T -> C	LOC_Os08g12880.1	downstream_gene_variant ; 2472.0bp to feature; MODIFIER	silent_mutation	Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0807648774	T -> C	LOC_Os08g12880-LOC_Os08g12890	intergenic_region ; MODIFIER	silent_mutation	Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N
vg0807648774	T -> DEL	N	N	silent_mutation	Average:45.807; most accessible tissue: Minghui63 flag leaf, score: 73.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807648774	1.01E-06	NA	mr1350_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
vg0807648774	3.09E-06	NA	mr1350_2	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