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Detailed information for vg1208976538:

Variant ID: vg1208976538 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8976538
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTGATCAATGATTGAAGCGATCGGGAAGGTTAGTCGTCGTTCCGCTATATCGGCTAACTTTTATAACAAGTGGTATCAGAGCAGAAGGTTTCAGCATT[A/G]
GATCAAGAAGACATGTGGAGGAGGAAACACGAGGTGGGGATCACGCATCGACATGAGATCGTCAGCCGTGGCGATGAGATCGATGGCGACAACGAGGATG

Reverse complement sequence

CATCCTCGTTGTCGCCATCGATCTCATCGCCACGGCTGACGATCTCATGTCGATGCGTGATCCCCACCTCGTGTTTCCTCCTCCACATGTCTTCTTGATC[T/C]
AATGCTGAAACCTTCTGCTCTGATACCACTTGTTATAAAAGTTAGCCGATATAGCGGAACGACGACTAACCTTCCCGATCGCTTCAATCATTGATCACCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.30%	0.20%	2.01%	20.42%	NA
All Indica	2759	63.40%	0.40%	3.12%	33.09%	NA
All Japonica	1512	98.90%	0.00%	0.07%	0.99%	NA
Aus	269	87.40%	0.00%	2.23%	10.41%	NA
Indica I	595	55.60%	0.20%	2.35%	41.85%	NA
Indica II	465	62.80%	0.20%	3.01%	33.98%	NA
Indica III	913	67.90%	0.30%	3.61%	28.15%	NA
Indica Intermediate	786	64.50%	0.60%	3.18%	31.68%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	91.10%	1.10%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208976538	A -> DEL	N	N	silent_mutation	Average:29.201; most accessible tissue: Minghui63 flag leaf, score: 57.881	N	N	N	N
vg1208976538	A -> G	LOC_Os12g15700.1	upstream_gene_variant ; 1725.0bp to feature; MODIFIER	silent_mutation	Average:29.201; most accessible tissue: Minghui63 flag leaf, score: 57.881	N	N	N	N
vg1208976538	A -> G	LOC_Os12g15700-LOC_Os12g15730	intergenic_region ; MODIFIER	silent_mutation	Average:29.201; most accessible tissue: Minghui63 flag leaf, score: 57.881	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208976538	6.00E-06	NA	mr1364_2	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
vg1208976538	2.04E-06	3.01E-07	mr1364_2	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