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Detailed information for vg1123663718:

Variant ID: vg1123663718 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23663718
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTGTACTATGGCATACTAATCCTGGAACTAAAACTCCTTTCTTTACTTGAAACTCAGGTACTTCTTCTTGGCTCTTGCTCTACTGGTACTGCTTCCT[G/A]
CCATCTTTCTTGATCTGCTGACTGCTACTGGTGATTCTCTTCCTCCTCTTGAAGCCGTCCCCTTGCTGATCTTTGCTCCATCTTGCTTCTTGACTTGAGT

Reverse complement sequence

ACTCAAGTCAAGAAGCAAGATGGAGCAAAGATCAGCAAGGGGACGGCTTCAAGAGGAGGAAGAGAATCACCAGTAGCAGTCAGCAGATCAAGAAAGATGG[C/T]
AGGAAGCAGTACCAGTAGAGCAAGAGCCAAGAAGAAGTACCTGAGTTTCAAGTAAAGAAAGGAGTTTTAGTTCCAGGATTAGTATGCCATAGTACAAATC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.60%	7.50%	0.87%	4.04%	NA
All Indica	2759	80.10%	12.60%	1.30%	6.05%	NA
All Japonica	1512	99.50%	0.10%	0.13%	0.33%	NA
Aus	269	98.90%	0.00%	0.00%	1.12%	NA
Indica I	595	88.60%	7.70%	0.34%	3.36%	NA
Indica II	465	83.00%	2.80%	2.37%	11.83%	NA
Indica III	913	70.90%	21.00%	2.08%	6.02%	NA
Indica Intermediate	786	82.60%	12.20%	0.51%	4.71%	NA
Temperate Japonica	767	99.50%	0.00%	0.13%	0.39%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	84.40%	2.10%	2.08%	11.46%	NA
Intermediate	90	86.70%	6.70%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123663718	G -> A	LOC_Os11g39720.1	downstream_gene_variant ; 2549.0bp to feature; MODIFIER	silent_mutation	Average:50.995; most accessible tissue: Zhenshan97 flower, score: 86.118	N	N	N	N
vg1123663718	G -> A	LOC_Os11g39720-LOC_Os11g39730	intergenic_region ; MODIFIER	silent_mutation	Average:50.995; most accessible tissue: Zhenshan97 flower, score: 86.118	N	N	N	N
vg1123663718	G -> DEL	N	N	silent_mutation	Average:50.995; most accessible tissue: Zhenshan97 flower, score: 86.118	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123663718	4.41E-06	NA	mr1528_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
vg1123663718	1.34E-06	3.40E-06	mr1528_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