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Detailed information for vg1215800897:

Variant ID: vg1215800897 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15800897
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAGACGGCCGACCTAGTGCCTAGGCGGAAGCCACCAAGAACTACATACGTCACAGCGGTTGGGTTGTGTGGGATAACGTGCCTGTCAGTACGGTGTACT[G/A]
GCGCAGAACAAGGGCACACGGAGATCATGAGAGCTTTGTCCCATATTCGGAGAAAGAGATGTTGTGGACCACAATGCTCGAGACATTCACCCTTCCCACA

Reverse complement sequence

TGTGGGAAGGGTGAATGTCTCGAGCATTGTGGTCCACAACATCTCTTTCTCCGAATATGGGACAAAGCTCTCATGATCTCCGTGTGCCCTTGTTCTGCGC[C/T]
AGTACACCGTACTGACAGGCACGTTATCCCACACAACCCAACCGCTGTGACGTATGTAGTTCTTGGTGGCTTCCGCCTAGGCACTAGGTCGGCCGTCTTC

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	84.60%	15.30%	0.06%	0.00%	NA
All Indica	2759	74.20%	25.70%	0.11%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	87.90%	12.10%	0.00%	0.00%	NA
Indica II	465	93.80%	6.00%	0.22%	0.00%	NA
Indica III	913	51.90%	48.00%	0.11%	0.00%	NA
Indica Intermediate	786	78.00%	21.90%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	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
vg1215800897	G -> A	LOC_Os12g26980.1	upstream_gene_variant ; 3889.0bp to feature; MODIFIER	silent_mutation	Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1215800897	G -> A	LOC_Os12g26970.1	downstream_gene_variant ; 2704.0bp to feature; MODIFIER	silent_mutation	Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg1215800897	G -> A	LOC_Os12g26970-LOC_Os12g26980	intergenic_region ; MODIFIER	silent_mutation	Average:39.572; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215800897	1.26E-06	NA	mr1438	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
vg1215800897	6.54E-06	NA	mr1438	Ind_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