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Detailed information for vg1101962356:

Variant ID: vg1101962356 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 1962356
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCCGAGTCTGTTTCCTCCAAGTCCCCACCCCCACGTGATTCCCATATTACCATCCCACTTCGGTGGAGTCGACTCCTTGTCTCTCTTCTCTCGGTTTA[G/T]
ATCCATACCGTGTCTTCCCACATAGCTAGGTGAGAATTTTTGAAGTGTCGGATTGGAGATCCGTTTGCAAAAACGGAACCTTCGGGACGAGTACATTCCA

Reverse complement sequence

TGGAATGTACTCGTCCCGAAGGTTCCGTTTTTGCAAACGGATCTCCAATCCGACACTTCAAAAATTCTCACCTAGCTATGTGGGAAGACACGGTATGGAT[C/A]
TAAACCGAGAGAAGAGAGACAAGGAGTCGACTCCACCGAAGTGGGATGGTAATATGGGAATCACGTGGGGGTGGGGACTTGGAGGAAACAGACTCGGCTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.10%	1.00%	0.91%	0.00%	NA
All Indica	2759	96.90%	1.60%	1.52%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	96.60%	2.00%	1.34%	0.00%	NA
Indica II	465	96.30%	1.70%	1.94%	0.00%	NA
Indica III	913	98.10%	0.90%	0.99%	0.00%	NA
Indica Intermediate	786	95.90%	2.00%	2.04%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg1101962356	G -> T	LOC_Os11g04620.1	upstream_gene_variant ; 809.0bp to feature; MODIFIER	N	Average:50.958; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N
vg1101962356	G -> T	LOC_Os11g04610.1	downstream_gene_variant ; 704.0bp to feature; MODIFIER	N	Average:50.958; most accessible tissue: Zhenshan97 flag leaf, score: 81.212	N	N	N	N
vg1101962356	G -> T	LOC_Os11g04610-LOC_Os11g04620	intergenic_region ; MODIFIER	N	Average:50.958; 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
vg1101962356	3.39E-06	NA	mr1165	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
vg1101962356	2.41E-06	NA	mr1478	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