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Detailed information for vg0620202115:

Variant ID: vg0620202115 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20202115
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCGTGGGCGCGAGAAACGAGGGAGCGAGATAGTGGGCGCGAGAAGCGAGGAGCCGAGCACAGCGTTGGCAAGGGTATAAAGACACCGAGGAAGGGATTT[A/G]
CTTCCTTCCTCTCGCCATTATTCCCCTTGTCTTCGCCGCTTGCGCCCTAACTCCTTGTTTCCTGTGCCCTACCCTCGCCACACGCGCTCGCTCTCAAACA

Reverse complement sequence

TGTTTGAGAGCGAGCGCGTGTGGCGAGGGTAGGGCACAGGAAACAAGGAGTTAGGGCGCAAGCGGCGAAGACAAGGGGAATAATGGCGAGAGGAAGGAAG[T/C]
AAATCCCTTCCTCGGTGTCTTTATACCCTTGCCAACGCTGTGCTCGGCTCCTCGCTTCTCGCGCCCACTATCTCGCTCCCTCGTTTCTCGCGCCCACGCT

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	33.90%	1.30%	20.84%	43.93%	NA
All Indica	2759	7.10%	2.00%	19.10%	71.77%	NA
All Japonica	1512	86.70%	0.10%	9.52%	3.70%	NA
Aus	269	1.10%	2.20%	91.82%	4.83%	NA
Indica I	595	7.90%	1.20%	11.26%	79.66%	NA
Indica II	465	10.10%	0.40%	19.78%	69.68%	NA
Indica III	913	2.60%	3.70%	24.75%	68.89%	NA
Indica Intermediate	786	10.10%	1.50%	18.07%	70.36%	NA
Temperate Japonica	767	83.20%	0.10%	11.99%	4.69%	NA
Tropical Japonica	504	92.50%	0.00%	4.37%	3.17%	NA
Japonica Intermediate	241	85.90%	0.00%	12.45%	1.66%	NA
VI/Aromatic	96	46.90%	0.00%	51.04%	2.08%	NA
Intermediate	90	51.10%	1.10%	20.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620202115	A -> G	LOC_Os06g34760.1	downstream_gene_variant ; 928.0bp to feature; MODIFIER	silent_mutation	Average:19.722; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0620202115	A -> G	LOC_Os06g34750-LOC_Os06g34760	intergenic_region ; MODIFIER	silent_mutation	Average:19.722; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N
vg0620202115	A -> DEL	N	N	silent_mutation	Average:19.722; most accessible tissue: Minghui63 root, score: 35.002	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620202115	NA	1.49E-06	mr1796	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
vg0620202115	3.26E-06	3.26E-06	mr1971_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