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Detailed information for vg0111998777:

Variant ID: vg0111998777 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11998777
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAGGGATCTTGGGTGGATGTGAGGATCTTGAGTGGATGTGATGTGAGGATCTTGAGTGGAGGTGACACATCCTAATACAATAAATCTAGATAGAACAT[C/T]
CACCCAAGATCCCTTATATTAGGGGATAGAGAGAGTAGCATTCTATGCTCCTTATAGTCAACTATATATGGTTGTAGTAGTGTTACCTCACTGGTGGAGA

Reverse complement sequence

TCTCCACCAGTGAGGTAACACTACTACAACCATATATAGTTGACTATAAGGAGCATAGAATGCTACTCTCTCTATCCCCTAATATAAGGGATCTTGGGTG[G/A]
ATGTTCTATCTAGATTTATTGTATTAGGATGTGTCACCTCCACTCAAGATCCTCACATCACATCCACTCAAGATCCTCACATCCACCCAAGATCCCTTAT

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	51.20%	48.60%	0.17%	0.00%	NA
All Indica	2759	75.40%	24.40%	0.22%	0.00%	NA
All Japonica	1512	3.40%	96.60%	0.00%	0.00%	NA
Aus	269	62.80%	37.20%	0.00%	0.00%	NA
Indica I	595	85.40%	14.30%	0.34%	0.00%	NA
Indica II	465	91.60%	8.40%	0.00%	0.00%	NA
Indica III	913	66.20%	33.50%	0.33%	0.00%	NA
Indica Intermediate	786	69.10%	30.80%	0.13%	0.00%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	5.80%	94.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	76.00%	24.00%	0.00%	0.00%	NA
Intermediate	90	51.10%	46.70%	2.22%	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
vg0111998777	C -> T	LOC_Os01g21490.1	downstream_gene_variant ; 605.0bp to feature; MODIFIER	silent_mutation	Average:49.81; most accessible tissue: Zhenshan97 flower, score: 55.587	N	N	N	N
vg0111998777	C -> T	LOC_Os01g21480-LOC_Os01g21490	intergenic_region ; MODIFIER	silent_mutation	Average:49.81; most accessible tissue: Zhenshan97 flower, score: 55.587	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111998777	NA	2.76E-11	mr1553	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
vg0111998777	NA	1.62E-15	mr1553_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
vg0111998777	NA	7.06E-06	mr1553_2	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