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Detailed information for vg1201779595:

Variant ID: vg1201779595 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 1779595
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ACATAGCCCCACGACACGTTTCCGTGCGCCGACATGCCACCACGACATACCGGAAAGAGGCCGTGACAGGACCCTTCGCATAACCCCATCTAACCAAGCA[C/A]
ACCACACCTCAGGTTTCACCCCCCACTCCTCGCAAGGCAGCGGGCAGTCCCCTCTCGTGCCTAGGTGAATCCGGAAGCGACAGAGGCCGTCGCAGGGCCC

Reverse complement sequence

GGGCCCTGCGACGGCCTCTGTCGCTTCCGGATTCACCTAGGCACGAGAGGGGACTGCCCGCTGCCTTGCGAGGAGTGGGGGGTGAAACCTGAGGTGTGGT[G/T]
TGCTTGGTTAGATGGGGTTATGCGAAGGGTCCTGTCACGGCCTCTTTCCGGTATGTCGTGGTGGCATGTCGGCGCACGGAAACGTGTCGTGGGGCTATGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.00%	1.40%	19.19%	23.42%	NA
All Indica	2759	32.70%	2.10%	27.08%	38.20%	NA
All Japonica	1512	97.70%	0.00%	0.40%	1.92%	NA
Aus	269	39.00%	3.30%	54.28%	3.35%	NA
Indica I	595	32.30%	0.30%	23.53%	43.87%	NA
Indica II	465	22.60%	3.90%	20.65%	52.90%	NA
Indica III	913	37.30%	2.10%	32.64%	27.93%	NA
Indica Intermediate	786	33.50%	2.30%	27.10%	37.15%	NA
Temperate Japonica	767	96.10%	0.00%	0.39%	3.52%	NA
Tropical Japonica	504	99.20%	0.00%	0.40%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	76.70%	0.00%	8.89%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1201779595	C -> DEL	N	N	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04204.1	upstream_gene_variant ; 4876.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04210.1	upstream_gene_variant ; 1892.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04220.1	upstream_gene_variant ; 3980.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04204.2	upstream_gene_variant ; 4876.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04204.3	upstream_gene_variant ; 4876.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04204.4	upstream_gene_variant ; 4876.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04204.5	upstream_gene_variant ; 4876.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04210.2	upstream_gene_variant ; 1892.0bp to feature; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg1201779595	C -> A	LOC_Os12g04210-LOC_Os12g04220	intergenic_region ; MODIFIER	silent_mutation	Average:16.712; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1201779595	NA	3.12E-08	mr1050	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
vg1201779595	4.12E-06	NA	mr1348	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
vg1201779595	NA	8.46E-07	mr1892_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
vg1201779595	NA	2.88E-07	mr1892_2	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