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Detailed information for vg0316396025:

Variant ID: vg0316396025 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16396025
Reference Allele: A	Alternative Allele: C,T
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTGACGTCAGCATGACATCAGCACCCGATTTACGTGCAAAAACTACTTTAAACTGATTTTTCTCTTAAATTATTTATCCAAATCATGATTCGATTGCA[A/C,T]
CATTAAATTCATTGCAATTAAATCTTCAAAACAAGACCACACATGGATATATTCCGACGAAAAAAAAAATTAGCTTATTATTGAATTATTTTTAAATGTT

Reverse complement sequence

AACATTTAAAAATAATTCAATAATAAGCTAATTTTTTTTTTCGTCGGAATATATCCATGTGTGGTCTTGTTTTGAAGATTTAATTGCAATGAATTTAATG[T/G,A]
TGCAATCGAATCATGATTTGGATAAATAATTTAAGAGAAAAATCAGTTTAAAGTAGTTTTTGCACGTAAATCGGGTGCTGATGTCATGCTGACGTCAGCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.70%	18.30%	0.70%	56.22%	NA
All Indica	2759	16.70%	6.90%	0.80%	75.68%	NA
All Japonica	1512	39.80%	38.30%	0.46%	21.43%	NA
Aus	269	1.90%	27.10%	0.37%	70.63%	NA
Indica I	595	39.00%	2.20%	1.01%	57.82%	NA
Indica II	465	7.10%	1.90%	0.65%	90.32%	NA
Indica III	913	9.00%	8.90%	0.11%	82.04%	NA
Indica Intermediate	786	14.40%	10.90%	1.53%	73.16%	NA
Temperate Japonica	767	49.80%	49.70%	0.00%	0.52%	NA
Tropical Japonica	504	26.40%	12.70%	1.39%	59.52%	NA
Japonica Intermediate	241	36.10%	55.60%	0.00%	8.30%	NA
VI/Aromatic	96	83.30%	6.20%	0.00%	10.42%	NA
Intermediate	90	24.40%	22.20%	3.33%	50.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0316396025	A -> C	LOC_Os03g28910.1	downstream_gene_variant ; 1221.0bp to feature; MODIFIER	silent_mutation	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> C	LOC_Os03g28920.1	downstream_gene_variant ; 4554.0bp to feature; MODIFIER	silent_mutation	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> C	LOC_Os03g28410-LOC_Os03g28910	intergenic_region ; MODIFIER	silent_mutation	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> DEL	N	N	silent_mutation	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> T	LOC_Os03g28910.1	downstream_gene_variant ; 1221.0bp to feature; MODIFIER	N	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> T	LOC_Os03g28920.1	downstream_gene_variant ; 4554.0bp to feature; MODIFIER	N	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0316396025	A -> T	LOC_Os03g28410-LOC_Os03g28910	intergenic_region ; MODIFIER	N	Average:29.393; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316396025	7.16E-06	7.16E-06	mr1342	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
vg0316396025	NA	4.33E-06	mr1910	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