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Detailed information for vg0706437051:

Variant ID: vg0706437051 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6437051
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGTATACATATTTGTGCCAATTATAACGTATGTACCTACATTCTAGAGGTATATGTAGGATCGAAACACAAGAACTAAGCCAACCAGAGGGGGTGAAT[G/A,T]
GTTGGTATACCCAAAAACCTAAAACTTTTAGCGGAAATAAAAGTTACCATCGAAATCGATGGATTGCGGTCTGACCAAAGTAGTTGCGCCGGTCTCACCG

Reverse complement sequence

CGGTGAGACCGGCGCAACTACTTTGGTCAGACCGCAATCCATCGATTTCGATGGTAACTTTTATTTCCGCTAAAAGTTTTAGGTTTTTGGGTATACCAAC[C/T,A]
ATTCACCCCCTCTGGTTGGCTTAGTTCTTGTGTTTCGATCCTACATATACCTCTAGAATGTAGGTACATACGTTATAATTGGCACAAATATGTATACCTC

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	80.20%	7.10%	2.20%	10.35%	T: 0.17%
All Indica	2759	83.50%	1.10%	1.96%	13.48%	NA
All Japonica	1512	86.00%	13.20%	0.13%	0.13%	T: 0.53%
Aus	269	41.30%	3.00%	17.10%	38.66%	NA
Indica I	595	86.20%	0.00%	2.52%	11.26%	NA
Indica II	465	96.60%	0.40%	0.43%	2.58%	NA
Indica III	913	78.60%	0.70%	1.75%	18.95%	NA
Indica Intermediate	786	79.30%	2.80%	2.67%	15.27%	NA
Temperate Japonica	767	93.10%	6.60%	0.13%	0.13%	NA
Tropical Japonica	504	88.70%	9.50%	0.20%	0.00%	T: 1.59%
Japonica Intermediate	241	57.70%	41.90%	0.00%	0.41%	NA
VI/Aromatic	96	7.30%	88.50%	0.00%	4.17%	NA
Intermediate	90	76.70%	13.30%	2.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706437051	G -> DEL	N	N	silent_mutation	Average:40.16; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg0706437051	G -> A	LOC_Os07g11650.1	upstream_gene_variant ; 3881.0bp to feature; MODIFIER	silent_mutation	Average:40.16; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg0706437051	G -> A	LOC_Os07g11650-LOC_Os07g11670	intergenic_region ; MODIFIER	silent_mutation	Average:40.16; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg0706437051	G -> T	LOC_Os07g11650.1	upstream_gene_variant ; 3881.0bp to feature; MODIFIER	silent_mutation	Average:40.16; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg0706437051	G -> T	LOC_Os07g11650-LOC_Os07g11670	intergenic_region ; MODIFIER	silent_mutation	Average:40.16; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706437051	1.09E-06	NA	mr1134	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
vg0706437051	NA	2.15E-08	mr1567_2	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