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Detailed information for vg0711760152:

Variant ID: vg0711760152 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11760152
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAATGCTGCTTTCGCAAATGAGCCTATATTATGCCATCCTTTGGTATCCTTGTGCACTTGCATATTTTGCTGTGTGGCTTGTTGAGTATGTCATATGCTC[A/T]
TTCTTGCAATAATCATCAAACCTCAGTTGAAGAAAAAGGATCCAGAAGGAGAAGACCTTTGGCTTAGATCCCAGTTGAGCTGCCTGTGGGAGTGGAGCTG

Reverse complement sequence

CAGCTCCACTCCCACAGGCAGCTCAACTGGGATCTAAGCCAAAGGTCTTCTCCTTCTGGATCCTTTTTCTTCAACTGAGGTTTGATGATTATTGCAAGAA[T/A]
GAGCATATGACATACTCAACAAGCCACACAGCAAAATATGCAAGTGCACAAGGATACCAAAGGATGGCATAATATAGGCTCATTTGCGAAAGCAGCATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.00%	3.40%	1.52%	2.07%	NA
All Indica	2759	99.70%	0.20%	0.11%	0.04%	NA
All Japonica	1512	80.00%	10.20%	4.17%	5.62%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.00%	0.38%	0.13%	NA
Temperate Japonica	767	64.30%	17.50%	7.30%	10.95%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	7.10%	2.90%	0.41%	NA
VI/Aromatic	96	83.30%	0.00%	5.21%	11.46%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0711760152	A -> DEL	N	N	silent_mutation	Average:48.636; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0711760152	A -> T	LOC_Os07g20370.1	upstream_gene_variant ; 1534.0bp to feature; MODIFIER	silent_mutation	Average:48.636; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N
vg0711760152	A -> T	LOC_Os07g20360-LOC_Os07g20370	intergenic_region ; MODIFIER	silent_mutation	Average:48.636; most accessible tissue: Zhenshan97 flag leaf, score: 75.455	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711760152	3.54E-06	5.60E-08	mr1182	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
vg0711760152	NA	9.33E-06	mr1282	Jap_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
vg0711760152	2.64E-06	1.21E-07	mr1650	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