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Detailed information for vg0819590125:

Variant ID: vg0819590125 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19590125
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACATCATAAGCATGGGTTAATCTAAAACCGACATAGACACAAATGAGCTTTTTCCCGTCATTCTAAGCCTTAGAGGGGTAAAAATTTAAAACTGGCAC[C/A]
TATAACACCTTGTAGGTACTGGTTTATTAAAAGAACCGGTTCATATAATTCCCATGCCTGTTTTTTTAATGAGTAAATTACACTATGGTCCTTAAACTTG

Reverse complement sequence

CAAGTTTAAGGACCATAGTGTAATTTACTCATTAAAAAAACAGGCATGGGAATTATATGAACCGGTTCTTTTAATAAACCAGTACCTACAAGGTGTTATA[G/T]
GTGCCAGTTTTAAATTTTTACCCCTCTAAGGCTTAGAATGACGGGAAAAAGCTCATTTGTGTCTATGTCGGTTTTAGATTAACCCATGCTTATGATGTGT

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	54.40%	5.60%	26.28%	13.67%	NA
All Indica	2759	30.20%	9.40%	39.94%	20.44%	NA
All Japonica	1512	93.50%	0.00%	4.30%	2.25%	NA
Aus	269	74.00%	0.00%	14.87%	11.15%	NA
Indica I	595	32.80%	2.40%	50.25%	14.62%	NA
Indica II	465	20.60%	3.90%	45.38%	30.11%	NA
Indica III	913	35.30%	14.70%	31.11%	18.95%	NA
Indica Intermediate	786	28.00%	12.00%	39.19%	20.87%	NA
Temperate Japonica	767	99.50%	0.00%	0.26%	0.26%	NA
Tropical Japonica	504	84.30%	0.00%	10.12%	5.56%	NA
Japonica Intermediate	241	93.40%	0.00%	4.98%	1.66%	NA
VI/Aromatic	96	71.90%	1.00%	14.58%	12.50%	NA
Intermediate	90	65.60%	4.40%	23.33%	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
vg0819590125	C -> A	LOC_Os08g31630-LOC_Os08g31649	intergenic_region ; MODIFIER	silent_mutation	Average:51.709; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg0819590125	C -> DEL	N	N	silent_mutation	Average:51.709; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819590125	3.56E-06	8.04E-09	mr1672_2	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
vg0819590125	NA	4.50E-06	mr1996_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