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Detailed information for vg1209696070:

Variant ID: vg1209696070 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9696070
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGTACAATATGATCAAATGTAAAGCATGACTTGCCTGTCTCTCGCACTGATGAGACCTCAGCAACGTCTTCGAGAAACCGCGGATCGACGAAACGGCCG[A/G]
AATCTACGCGACAAACAAAGCACACAAGCAAAACATGCTATAAGACTACTGAAACAGGAAACAAAATCATTTTAATGGATTCTTTGCATTTTTATGAATT

Reverse complement sequence

AATTCATAAAAATGCAAAGAATCCATTAAAATGATTTTGTTTCCTGTTTCAGTAGTCTTATAGCATGTTTTGCTTGTGTGCTTTGTTTGTCGCGTAGATT[T/C]
CGGCCGTTTCGTCGATCCGCGGTTTCTCGAAGACGTTGCTGAGGTCTCATCAGTGCGAGAGACAGGCAAGTCATGCTTTACATTTGATCATATTGTACCC

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	73.60%	1.40%	2.26%	22.75%	NA
All Indica	2759	61.60%	0.00%	2.83%	35.56%	NA
All Japonica	1512	91.20%	4.30%	1.46%	3.04%	NA
Aus	269	86.60%	0.00%	0.37%	13.01%	NA
Indica I	595	81.30%	0.00%	4.71%	13.95%	NA
Indica II	465	71.20%	0.00%	1.29%	27.53%	NA
Indica III	913	39.00%	0.00%	2.08%	58.93%	NA
Indica Intermediate	786	67.30%	0.00%	3.18%	29.52%	NA
Temperate Japonica	767	83.60%	8.30%	2.87%	5.22%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	99.20%	0.40%	0.00%	0.41%	NA
VI/Aromatic	96	86.50%	0.00%	6.25%	7.29%	NA
Intermediate	90	92.20%	1.10%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209696070	A -> DEL	N	N	silent_mutation	Average:35.996; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1209696070	A -> G	LOC_Os12g16910.1	upstream_gene_variant ; 1036.0bp to feature; MODIFIER	silent_mutation	Average:35.996; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1209696070	A -> G	LOC_Os12g16900.1	downstream_gene_variant ; 1209.0bp to feature; MODIFIER	silent_mutation	Average:35.996; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1209696070	A -> G	LOC_Os12g16920.1	downstream_gene_variant ; 4334.0bp to feature; MODIFIER	silent_mutation	Average:35.996; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N
vg1209696070	A -> G	LOC_Os12g16900-LOC_Os12g16910	intergenic_region ; MODIFIER	silent_mutation	Average:35.996; most accessible tissue: Minghui63 flag leaf, score: 68.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209696070	NA	4.56E-06	mr1346_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
vg1209696070	NA	6.24E-07	mr1456_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