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Detailed information for vg0505502303:

Variant ID: vg0505502303 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5502303
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGCTTCAGCTCCACTCCCACAGGCAGCTCAACTGGGGTATAAGCCAAACGTCTTCTCCTTCTAGATCTTTTTTCTTCAACTGAGGTTGATTGATTATT[G/A]
CAAGGTGAGCATATGACATACTCAACAAGCCACACAGCAAATATGCCCATGCTGCTCAGGCCCAACTATTCTGAACAACCATACCCGGCTGTACAGATCT

Reverse complement sequence

AGATCTGTACAGCCGGGTATGGTTGTTCAGAATAGTTGGGCCTGAGCAGCATGGGCATATTTGCTGTGTGGCTTGTTGAGTATGTCATATGCTCACCTTG[C/T]
AATAATCAATCAACCTCAGTTGAAGAAAAAAGATCTAGAAGGAGAAGACGTTTGGCTTATACCCCAGTTGAGCTGCCTGTGGGAGTGGAGCTGAAGCCAT

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	94.70%	5.10%	0.00%	0.21%	NA
All Indica	2759	99.60%	0.10%	0.00%	0.36%	NA
All Japonica	1512	84.60%	15.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.00%	0.00%	0.44%	NA
Indica Intermediate	786	99.10%	0.10%	0.00%	0.76%	NA
Temperate Japonica	767	76.50%	23.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	80.10%	19.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0505502303	G -> DEL	N	N	silent_mutation	Average:47.109; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	N	N	N	N
vg0505502303	G -> A	LOC_Os05g09720.1	upstream_gene_variant ; 467.0bp to feature; MODIFIER	silent_mutation	Average:47.109; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	N	N	N	N
vg0505502303	G -> A	LOC_Os05g09716-LOC_Os05g09720	intergenic_region ; MODIFIER	silent_mutation	Average:47.109; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505502303	5.58E-07	NA	mr1672_2	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