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Detailed information for vg1221482713:

Variant ID: vg1221482713 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21482713
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTAAACCAAGAACCATGCAAGTATTAGATCATAGACCGTTACCACTCGACGCGCTGCGCAGCGGAAGAAGGCGCTAAGAAGTCGAAGGAATTCTCGCGAA[G/A]
TAGCGCGCGTCGATGTAGAGAAAGTAGTCGATCGCACCGGCTCGACCTTCTCCTCCTCGTGCGTTCTCCTCGCCGTATTCCCACGCCGATCAGCACCGCA

Reverse complement sequence

TGCGGTGCTGATCGGCGTGGGAATACGGCGAGGAGAACGCACGAGGAGGAGAAGGTCGAGCCGGTGCGATCGACTACTTTCTCTACATCGACGCGCGCTA[C/T]
TTCGCGAGAATTCCTTCGACTTCTTAGCGCCTTCTTCCGCTGCGCAGCGCGTCGAGTGGTAACGGTCTATGATCTAATACTTGCATGGTTCTTGGTTTAC

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	93.80%	6.20%	0.00%	0.00%	NA
All Indica	2759	89.80%	10.20%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	86.10%	13.90%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	88.10%	11.90%	0.00%	0.00%	NA
Indica Intermediate	786	88.50%	11.50%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg1221482713	G -> A	LOC_Os12g35340.1	downstream_gene_variant ; 1638.0bp to feature; MODIFIER	silent_mutation	Average:71.495; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N
vg1221482713	G -> A	LOC_Os12g35340-LOC_Os12g35350	intergenic_region ; MODIFIER	silent_mutation	Average:71.495; most accessible tissue: Zhenshan97 root, score: 84.212	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221482713	4.60E-07	NA	mr1719	Ind_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