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Detailed information for vg0505490581:

Variant ID: vg0505490581 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5490581
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCGGTGGCACTACGGGTGACGAGGGAGCTCGGGAGTTGGGGAAAACGAAAGAGGACGCCAAGGGGATGCTATATATAGGCTTGGATTGAAGAGATCGG[G/A]
CTCCAACCGAGAGGAATCGAAGCCGGAAAATCTTCGGGTTAGTTTGGAGAGATAAACTCAAACGGACTCGATTTGGTTTATCCGGGAGAAATTGGTCTCT

Reverse complement sequence

AGAGACCAATTTCTCCCGGATAAACCAAATCGAGTCCGTTTGAGTTTATCTCTCCAAACTAACCCGAAGATTTTCCGGCTTCGATTCCTCTCGGTTGGAG[C/T]
CCGATCTCTTCAATCCAAGCCTATATATAGCATCCCCTTGGCGTCCTCTTTCGTTTTCCCCAACTCCCGAGCTCCCTCGTCACCCGTAGTGCCACCGCCA

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	91.80%	8.10%	0.04%	0.00%	NA
All Indica	2759	94.70%	5.20%	0.04%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	17.10%	82.90%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	95.50%	4.30%	0.22%	0.00%	NA
Indica III	913	93.40%	6.60%	0.00%	0.00%	NA
Indica Intermediate	786	92.00%	8.00%	0.00%	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	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0505490581	G -> A	LOC_Os05g09716.1	upstream_gene_variant ; 786.0bp to feature; MODIFIER	silent_mutation	Average:64.728; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N
vg0505490581	G -> A	LOC_Os05g09708-LOC_Os05g09716	intergenic_region ; MODIFIER	silent_mutation	Average:64.728; most accessible tissue: Zhenshan97 flag leaf, score: 80.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505490581	1.71E-06	4.80E-06	mr1265	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
vg0505490581	NA	1.40E-08	mr1348	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
vg0505490581	2.03E-06	NA	mr1528	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