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Detailed information for vg0628246864:

Variant ID: vg0628246864 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28246864
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCCTGGCCGCAGAACTTGTGTGATCGTGTACGGTCCTTCCCATTTAGGTGAGAGCTTGTTTCGCCCTGCTTGGCTTTGAACCCGTCGGAGGACGTAGTC[A/G]
CCGATCGAAAGCGTGCGTGCTCGGATGCGCTTCTCGTGGTAACGGCGAAGGGCCTGTTGGTAGCTGGCTGCTCGAACGGCAACTCGATCGCGATGTTCCT

Reverse complement sequence

AGGAACATCGCGATCGAGTTGCCGTTCGAGCAGCCAGCTACCAACAGGCCCTTCGCCGTTACCACGAGAAGCGCATCCGAGCACGCACGCTTTCGATCGG[T/C]
GACTACGTCCTCCGACGGGTTCAAAGCCAAGCAGGGCGAAACAAGCTCTCACCTAAATGGGAAGGACCGTACACGATCACACAAGTTCTGCGGCCAGGCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.30%	4.40%	2.31%	0.00%	NA
All Indica	2759	90.90%	6.20%	2.97%	0.00%	NA
All Japonica	1512	98.20%	1.50%	0.26%	0.00%	NA
Aus	269	91.80%	1.90%	6.32%	0.00%	NA
Indica I	595	88.90%	6.20%	4.87%	0.00%	NA
Indica II	465	84.10%	12.00%	3.87%	0.00%	NA
Indica III	913	96.90%	1.60%	1.42%	0.00%	NA
Indica Intermediate	786	89.30%	7.90%	2.80%	0.00%	NA
Temperate Japonica	767	98.30%	1.60%	0.13%	0.00%	NA
Tropical Japonica	504	97.60%	1.80%	0.60%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	10.00%	6.67%	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
vg0628246864	A -> G	LOC_Os06g46510.1	downstream_gene_variant ; 1071.0bp to feature; MODIFIER	silent_mutation	Average:26.098; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg0628246864	A -> G	LOC_Os06g46520.1	downstream_gene_variant ; 177.0bp to feature; MODIFIER	silent_mutation	Average:26.098; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg0628246864	A -> G	LOC_Os06g46530.1	downstream_gene_variant ; 3006.0bp to feature; MODIFIER	silent_mutation	Average:26.098; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg0628246864	A -> G	LOC_Os06g46510-LOC_Os06g46520	intergenic_region ; MODIFIER	silent_mutation	Average:26.098; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628246864	2.72E-06	3.57E-07	mr1053	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
vg0628246864	7.53E-06	NA	mr1053	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