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Detailed information for vg1215976560:

Variant ID: vg1215976560 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15976560
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGCATCAGCATGGATGCGGGAGGGCGGTGTCGCAGTGCTACAACGGTATTCGTGCGCTTATGGATTTATCTATGATTATAACAACTACCAACATGCGGC[G/A]
GAGGCAAGGTCACCCATCAGTAGCGTGGCGGAGTTTACCGCCATGTAGGAGAAGCCACCAGTCGGCGACGGCATAGTCGACTGGCAGTGGAGACGAGGTC

Reverse complement sequence

GACCTCGTCTCCACTGCCAGTCGACTATGCCGTCGCCGACTGGTGGCTTCTCCTACATGGCGGTAAACTCCGCCACGCTACTGATGGGTGACCTTGCCTC[C/T]
GCCGCATGTTGGTAGTTGTTATAATCATAGATAAATCCATAAGCGCACGAATACCGTTGTAGCACTGCGACACCGCCCTCCCGCATCCATGCTGATGCCC

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	91.40%	5.90%	1.08%	1.57%	NA
All Indica	2759	96.60%	0.40%	0.43%	2.61%	NA
All Japonica	1512	83.30%	14.10%	2.51%	0.07%	NA
Aus	269	92.90%	7.10%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	85.20%	0.20%	1.72%	12.90%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	97.50%	0.80%	0.25%	1.53%	NA
Temperate Japonica	767	87.10%	9.30%	3.65%	0.00%	NA
Tropical Japonica	504	90.30%	9.70%	0.00%	0.00%	NA
Japonica Intermediate	241	56.80%	38.60%	4.15%	0.41%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	84.40%	13.30%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215976560	G -> DEL	N	N	silent_mutation	Average:56.468; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N
vg1215976560	G -> A	LOC_Os12g27220.1	upstream_gene_variant ; 3059.0bp to feature; MODIFIER	silent_mutation	Average:56.468; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N
vg1215976560	G -> A	LOC_Os12g27230.1	downstream_gene_variant ; 1142.0bp to feature; MODIFIER	silent_mutation	Average:56.468; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N
vg1215976560	G -> A	LOC_Os12g27220-LOC_Os12g27230	intergenic_region ; MODIFIER	silent_mutation	Average:56.468; most accessible tissue: Zhenshan97 young leaf, score: 86.852	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215976560	3.93E-06	NA	mr1017	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
vg1215976560	2.10E-08	NA	mr1022	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
vg1215976560	3.03E-10	NA	mr1023	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
vg1215976560	1.88E-06	NA	mr1055	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
vg1215976560	5.65E-11	NA	mr1079	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
vg1215976560	1.03E-10	NA	mr1142	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
vg1215976560	NA	5.22E-06	mr1280	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
vg1215976560	NA	4.44E-06	mr1280	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
vg1215976560	2.20E-11	NA	mr1489	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
vg1215976560	7.00E-11	NA	mr1491	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
vg1215976560	2.50E-08	NA	mr1778	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
vg1215976560	3.31E-07	NA	mr1022_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
vg1215976560	1.89E-08	NA	mr1023_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
vg1215976560	1.06E-08	NA	mr1079_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
vg1215976560	1.42E-09	NA	mr1489_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
vg1215976560	5.69E-07	NA	mr1778_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