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Detailed information for vg1219377796:

Variant ID: vg1219377796 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19377796
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGTACCTACCGGCGGCGAGGTCGAGAAGCGGCCAGCGATGATGCAGGTGGCGATGGCGGTTGGGAGGGGAGATCGGTGGCAATGGCGTTTGTATGGAAT[A/G]
CAGTTTTGTTGCAATAGGGTTTGGGGGGAATGGGGAAGGGGATCGAGAGGGAGTGTGGGGTTTTGTGTGGAAATTAATTGGAAAGAAGAAGCAAATTAAA

Reverse complement sequence

TTTAATTTGCTTCTTCTTTCCAATTAATTTCCACACAAAACCCCACACTCCCTCTCGATCCCCTTCCCCATTCCCCCCAAACCCTATTGCAACAAAACTG[T/C]
ATTCCATACAAACGCCATTGCCACCGATCTCCCCTCCCAACCGCCATCGCCACCTGCATCATCGCTGGCCGCTTCTCGACCTCGCCGCCGGTAGGTACGT

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	73.80%	4.30%	0.70%	21.20%	NA
All Indica	2759	65.10%	2.60%	0.91%	31.39%	NA
All Japonica	1512	98.50%	0.90%	0.07%	0.60%	NA
Aus	269	16.70%	39.40%	2.23%	41.64%	NA
Indica I	595	67.60%	3.70%	1.18%	27.56%	NA
Indica II	465	30.80%	1.10%	1.29%	66.88%	NA
Indica III	913	79.70%	1.30%	0.66%	18.29%	NA
Indica Intermediate	786	66.40%	4.30%	0.76%	28.50%	NA
Temperate Japonica	767	99.10%	0.40%	0.13%	0.39%	NA
Tropical Japonica	504	99.00%	0.40%	0.00%	0.60%	NA
Japonica Intermediate	241	95.40%	3.30%	0.00%	1.24%	NA
VI/Aromatic	96	92.70%	4.20%	0.00%	3.12%	NA
Intermediate	90	78.90%	6.70%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219377796	A -> DEL	N	N	silent_mutation	Average:42.677; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1219377796	A -> G	LOC_Os12g32120.1	upstream_gene_variant ; 1482.0bp to feature; MODIFIER	silent_mutation	Average:42.677; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1219377796	A -> G	LOC_Os12g32130.1	upstream_gene_variant ; 3657.0bp to feature; MODIFIER	silent_mutation	Average:42.677; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N
vg1219377796	A -> G	LOC_Os12g32120-LOC_Os12g32130	intergenic_region ; MODIFIER	silent_mutation	Average:42.677; most accessible tissue: Zhenshan97 panicle, score: 73.605	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219377796	NA	8.43E-09	mr1060	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
vg1219377796	NA	2.60E-06	mr1319	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
vg1219377796	NA	7.66E-06	mr1400	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
vg1219377796	NA	2.67E-06	mr1444	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
vg1219377796	7.95E-06	NA	mr1579	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
vg1219377796	NA	3.01E-08	mr1621	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
vg1219377796	NA	1.24E-08	mr1937	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
vg1219377796	NA	9.92E-08	mr1582_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