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Detailed information for vg1101962366:

Variant ID: vg1101962366 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1962366
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTTTCCTCCAAGTCCCCACCCCCACGTGATTCCCATATTACCATCCCACTTCGGTGGAGTCGACTCCTTGTCTCTCTTCTCTCGGTTTAGATCCATACC[G/A]
TGTCTTCCCACATAGCTAGGTGAGAATTTTTGAAGTGTCGGATTGGAGATCCGTTTGCAAAAACGGAACCTTCGGGACGAGTACATTCCATTTTTGTATA

Reverse complement sequence

TATACAAAAATGGAATGTACTCGTCCCGAAGGTTCCGTTTTTGCAAACGGATCTCCAATCCGACACTTCAAAAATTCTCACCTAGCTATGTGGGAAGACA[C/T]
GGTATGGATCTAAACCGAGAGAAGAGAGACAAGGAGTCGACTCCACCGAAGTGGGATGGTAATATGGGAATCACGTGGGGGTGGGGACTTGGAGGAAACA

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	77.70%	1.00%	11.91%	9.37%	NA
All Indica	2759	64.80%	1.60%	19.10%	14.50%	NA
All Japonica	1512	99.10%	0.00%	0.26%	0.66%	NA
Aus	269	81.00%	0.70%	8.92%	9.29%	NA
Indica I	595	60.30%	2.00%	9.41%	28.24%	NA
Indica II	465	72.50%	1.70%	20.22%	5.59%	NA
Indica III	913	61.60%	0.80%	24.42%	13.25%	NA
Indica Intermediate	786	67.40%	2.20%	19.59%	10.81%	NA
Temperate Japonica	767	98.30%	0.00%	0.39%	1.30%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	4.17%	0.00%	NA
Intermediate	90	86.70%	0.00%	4.44%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1101962366	G -> A	LOC_Os11g04620.1	upstream_gene_variant ; 799.0bp to feature; MODIFIER	silent_mutation	Average:51.908; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N
vg1101962366	G -> A	LOC_Os11g04610.1	downstream_gene_variant ; 714.0bp to feature; MODIFIER	silent_mutation	Average:51.908; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N
vg1101962366	G -> A	LOC_Os11g04610-LOC_Os11g04620	intergenic_region ; MODIFIER	silent_mutation	Average:51.908; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N
vg1101962366	G -> DEL	N	N	silent_mutation	Average:51.908; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1101962366	1.65E-06	NA	mr1165	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
vg1101962366	3.02E-06	NA	mr1478	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