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Detailed information for vg1011136912:

Variant ID: vg1011136912 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11136912
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGAGGTACGAGAGATCGCTACGGCCTACTGGTCCAAGAACCAGGAGTAGCCTTATCTCTCGACCGATTGAAGTCGTGGTGCGAGGACCACTATGCTAC[T/A]
GGTCGAAGACTAGTCGTAGTCGTACCTCAACCATCTGAAGTCGTGGTGCGAGGACCGCTGCGCTACTGCTGTAGTCGTACCTCGACCATCTAATGTTAAG

Reverse complement sequence

CTTAACATTAGATGGTCGAGGTACGACTACAGCAGTAGCGCAGCGGTCCTCGCACCACGACTTCAGATGGTTGAGGTACGACTACGACTAGTCTTCGACC[A/T]
GTAGCATAGTGGTCCTCGCACCACGACTTCAATCGGTCGAGAGATAAGGCTACTCCTGGTTCTTGGACCAGTAGGCCGTAGCGATCTCTCGTACCTCGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.20%	2.20%	0.66%	8.97%	NA
All Indica	2759	95.80%	0.10%	0.69%	3.41%	NA
All Japonica	1512	92.70%	6.80%	0.00%	0.46%	NA
Aus	269	4.80%	0.00%	2.23%	92.94%	NA
Indica I	595	98.30%	0.20%	0.00%	1.51%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	94.50%	0.00%	1.75%	3.72%	NA
Indica Intermediate	786	93.30%	0.10%	0.38%	6.23%	NA
Temperate Japonica	767	91.00%	9.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.00%	0.00%	0.40%	NA
Japonica Intermediate	241	85.90%	12.00%	0.00%	2.07%	NA
VI/Aromatic	96	30.20%	0.00%	6.25%	63.54%	NA
Intermediate	90	86.70%	0.00%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1011136912	T -> A	LOC_Os10g21700-LOC_Os10g21720	intergenic_region ; MODIFIER	silent_mutation	Average:48.466; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N
vg1011136912	T -> DEL	N	N	silent_mutation	Average:48.466; most accessible tissue: Zhenshan97 young leaf, score: 74.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011136912	2.57E-06	2.57E-06	mr1566	Jap_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