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Detailed information for vg0620971322:

Variant ID: vg0620971322 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20971322
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAATAGTAGGGATGGTGCATGCATCGAGTTTGTTGCTAGAGTAAATATAGTATGAGAGAGCTATTAGCTTTTTTTTTGTCTTGGTGTACCTATGAAAT[A/G]
TATAGATCAATTTGGAATGGAAGGAAATTTTGTTAAGTTGTGTTAAATCACTATGTAAATTTTGTAGAAAACCAACACTTCATTAGTTGATTCATACCTT

Reverse complement sequence

AAGGTATGAATCAACTAATGAAGTGTTGGTTTTCTACAAAATTTACATAGTGATTTAACACAACTTAACAAAATTTCCTTCCATTCCAAATTGATCTATA[T/C]
ATTTCATAGGTACACCAAGACAAAAAAAAAGCTAATAGCTCTCTCATACTATATTTACTCTAGCAACAAACTCGATGCATGCACCATCCCTACTATTTCC

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	92.00%	7.20%	0.74%	0.00%	NA
All Indica	2759	87.40%	11.60%	1.05%	0.00%	NA
All Japonica	1512	99.60%	0.20%	0.20%	0.00%	NA
Aus	269	94.10%	5.60%	0.37%	0.00%	NA
Indica I	595	96.80%	2.40%	0.84%	0.00%	NA
Indica II	465	86.20%	11.80%	1.94%	0.00%	NA
Indica III	913	77.80%	21.70%	0.55%	0.00%	NA
Indica Intermediate	786	92.00%	6.70%	1.27%	0.00%	NA
Temperate Japonica	767	99.30%	0.30%	0.39%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620971322	A -> G	LOC_Os06g35940.1	downstream_gene_variant ; 304.0bp to feature; MODIFIER	silent_mutation	Average:42.178; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N
vg0620971322	A -> G	LOC_Os06g35930-LOC_Os06g35940	intergenic_region ; MODIFIER	silent_mutation	Average:42.178; most accessible tissue: Zhenshan97 young leaf, score: 50.669	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620971322	6.92E-09	NA	mr1695	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
vg0620971322	7.23E-08	1.41E-11	mr1695	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
vg0620971322	1.55E-09	NA	mr1695_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
vg0620971322	6.33E-10	6.78E-11	mr1695_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