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Detailed information for vg1011622635:

Variant ID: vg1011622635 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11622635
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TGATGTTGTGCCACGATCTATCTGTCTCGCTCTAGGGCTAGCCACGATTTGGGTTGGGTTGGGAACTTGGGGACGACTTATGGACTATTGATTCTATGTG[C/T]
CTTTTTAACTTCGGAATTCCGAAAAAAATTTTGGAATTTTTCGTACCGATTCCGAGTTCCAACGGAAACCGCTAATATCATATTTGATTCTGTTTCTGAG

Reverse complement sequence

CTCAGAAACAGAATCAAATATGATATTAGCGGTTTCCGTTGGAACTCGGAATCGGTACGAAAAATTCCAAAATTTTTTTCGGAATTCCGAAGTTAAAAAG[G/A]
CACATAGAATCAATAGTCCATAAGTCGTCCCCAAGTTCCCAACCCAACCCAAATCGTGGCTAGCCCTAGAGCGAGACAGATAGATCGTGGCACAACATCA

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	68.60%	31.20%	0.15%	0.00%	NA
All Indica	2759	47.80%	52.00%	0.14%	0.00%	NA
All Japonica	1512	98.50%	1.30%	0.20%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	29.60%	70.40%	0.00%	0.00%	NA
Indica II	465	47.50%	52.50%	0.00%	0.00%	NA
Indica III	913	57.70%	42.10%	0.22%	0.00%	NA
Indica Intermediate	786	50.40%	49.40%	0.25%	0.00%	NA
Temperate Japonica	767	98.30%	1.30%	0.39%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	76.70%	23.30%	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
vg1011622635	C -> T	LOC_Os10g22440.1	upstream_gene_variant ; 4713.0bp to feature; MODIFIER	silent_mutation	Average:42.839; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg1011622635	C -> T	LOC_Os10g22450.1	upstream_gene_variant ; 1757.0bp to feature; MODIFIER	silent_mutation	Average:42.839; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N
vg1011622635	C -> T	LOC_Os10g22440-LOC_Os10g22450	intergenic_region ; MODIFIER	silent_mutation	Average:42.839; most accessible tissue: Zhenshan97 young leaf, score: 56.533	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011622635	NA	7.57E-06	mr1661	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
vg1011622635	NA	5.27E-09	mr1770	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
vg1011622635	NA	9.11E-07	mr1834_2	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