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Detailed information for vg0606129619:

Variant ID: vg0606129619 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 6129619
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCAGGGGAGCTAAGGTAGCCATCCAACTCTTCCGTCGAGACTGTCCCAAGAGGTTGGAGTATAACGCCAACCTCTCTGGATCTAGATTGGATCGGGGCC[G/A]
AAGCCGGAGCTTGTCTAGATCTTCGAGTGGGAGATGTCTTGGCTGTGAAGACAGCGGCCAAATCATCAGGAAGTCTCATCAGGATTGAGGGATAGAACCC

Reverse complement sequence

GGGTTCTATCCCTCAATCCTGATGAGACTTCCTGATGATTTGGCCGCTGTCTTCACAGCCAAGACATCTCCCACTCGAAGATCTAGACAAGCTCCGGCTT[C/T]
GGCCCCGATCCAATCTAGATCCAGAGAGGTTGGCGTTATACTCCAACCTCTTGGGACAGTCTCGACGGAAGAGTTGGATGGCTACCTTAGCTCCCCTGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.10%	4.50%	8.29%	0.11%	NA
All Indica	2759	82.60%	5.60%	11.67%	0.18%	NA
All Japonica	1512	96.40%	1.30%	2.25%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	84.00%	3.90%	11.93%	0.17%	NA
Indica II	465	83.20%	7.50%	9.03%	0.22%	NA
Indica III	913	82.00%	5.60%	12.05%	0.33%	NA
Indica Intermediate	786	81.70%	5.70%	12.60%	0.00%	NA
Temperate Japonica	767	95.30%	2.00%	2.74%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	92.90%	2.10%	4.98%	0.00%	NA
VI/Aromatic	96	24.00%	42.70%	33.33%	0.00%	NA
Intermediate	90	95.60%	0.00%	4.44%	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
vg0606129619	G -> A	LOC_Os06g11560.1	upstream_gene_variant ; 218.0bp to feature; MODIFIER	silent_mutation	Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0606129619	G -> A	LOC_Os06g11570.1	upstream_gene_variant ; 2284.0bp to feature; MODIFIER	silent_mutation	Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0606129619	G -> A	LOC_Os06g11560-LOC_Os06g11570	intergenic_region ; MODIFIER	silent_mutation	Average:17.284; most accessible tissue: Zhenshan97 root, score: 32.766	N	N	N	N
vg0606129619	G -> DEL	N	N	silent_mutation	Average:17.284; 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
vg0606129619	3.40E-06	NA	mr1795	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
vg0606129619	NA	2.22E-06	mr1795_2	Jap_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
vg0606129619	NA	1.79E-06	mr1913_2	Jap_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