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Detailed information for vg0216565123:

Variant ID: vg0216565123 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 16565123
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAGGGGGTTATGAACCGGGAGTAAAGCCCCTTTCTCCACCAGTGACTGGGACATGCAAAGGTGCTTGTTCTTTGGTTTCCCTAAGTGCATAGTGAAGTT[C/A]
TAGGGCTTCGATCATGTCTGCTACCATATGCAGCACTACTGATGCAGTGATGGGTCACCGTTCGTTGAGACTCTTTCAGAATTGTTTCAGGAGATTAGCA

Reverse complement sequence

TGCTAATCTCCTGAAACAATTCTGAAAGAGTCTCAACGAACGGTGACCCATCACTGCATCAGTAGTGCTGCATATGGTAGCAGACATGATCGAAGCCCTA[G/T]
AACTTCACTATGCACTTAGGGAAACCAAAGAACAAGCACCTTTGCATGTCCCAGTCACTGGTGGAGAAAGGGGCTTTACTCCCGGTTCATAACCCCCTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.40%	6.50%	1.08%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.14%	0.00%	NA
All Japonica	1512	76.90%	20.00%	3.11%	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	99.60%	0.10%	0.33%	0.00%	NA
Indica Intermediate	786	99.60%	0.30%	0.13%	0.00%	NA
Temperate Japonica	767	78.00%	17.50%	4.56%	0.00%	NA
Tropical Japonica	504	87.30%	12.50%	0.20%	0.00%	NA
Japonica Intermediate	241	51.90%	43.60%	4.56%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0216565123	C -> A	LOC_Os02g27980.1	upstream_gene_variant ; 3257.0bp to feature; MODIFIER	silent_mutation	Average:58.214; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0216565123	C -> A	LOC_Os02g27970.1	downstream_gene_variant ; 2949.0bp to feature; MODIFIER	silent_mutation	Average:58.214; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N
vg0216565123	C -> A	LOC_Os02g27970-LOC_Os02g27980	intergenic_region ; MODIFIER	silent_mutation	Average:58.214; most accessible tissue: Zhenshan97 panicle, score: 68.538	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0216565123	NA	1.03E-06	mr1807_2	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
vg0216565123	3.00E-07	3.00E-07	mr1914_2	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