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Detailed information for vg0508292114:

Variant ID: vg0508292114 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 8292114
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTCTTGCACCTTTGGCCTTTGCTATTGCCGCTATCACTGGTGGAGAAACCCTTTATAGTCCCGGTTCGTAACCTCCCTTTAGTCCCGGTTTCTAAACC[G/A]
GGACTACCAATCCGGGACTAAAGATCGCTATCTTTGGTACACCAACCGGGACGAAAGATCGATCTTTAGTCCCGGTTGGGGTTACTAACCGGGACTAAAG

Reverse complement sequence

CTTTAGTCCCGGTTAGTAACCCCAACCGGGACTAAAGATCGATCTTTCGTCCCGGTTGGTGTACCAAAGATAGCGATCTTTAGTCCCGGATTGGTAGTCC[C/T]
GGTTTAGAAACCGGGACTAAAGGGAGGTTACGAACCGGGACTATAAAGGGTTTCTCCACCAGTGATAGCGGCAATAGCAAAGGCCAAAGGTGCAAGACAA

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	97.90%	2.10%	0.00%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.50%	6.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	91.80%	8.20%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	14.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	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
vg0508292114	G -> A	LOC_Os05g14560.1	downstream_gene_variant ; 471.0bp to feature; MODIFIER	silent_mutation	Average:49.651; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N
vg0508292114	G -> A	LOC_Os05g14540-LOC_Os05g14560	intergenic_region ; MODIFIER	silent_mutation	Average:49.651; most accessible tissue: Zhenshan97 root, score: 62.394	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0508292114	1.00E-07	1.00E-07	mr1412	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
vg0508292114	NA	5.30E-06	mr1686	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