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Detailed information for vg0620500908:

Variant ID: vg0620500908 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20500908
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTATTAAGATCGAATAAAATTTGAATAGATATCTTTATTTTTAACGTTTTGCGTTTATATACATGCATGAGAAAGAGAGTTACGAAAATATACCTCTAC[C/T]
GCAGAAGGAAGATGCGGGAATGAGACAGTGCCGCTGGCTCCCGCGCAGCGTCCATGCGGCGCTATCGCTCCCGTGGAACGTCGGCGCGGAATCAGCGTGG

Reverse complement sequence

CCACGCTGATTCCGCGCCGACGTTCCACGGGAGCGATAGCGCCGCATGGACGCTGCGCGGGAGCCAGCGGCACTGTCTCATTCCCGCATCTTCCTTCTGC[G/A]
GTAGAGGTATATTTTCGTAACTCTCTTTCTCATGCATGTATATAAACGCAAAACGTTAAAAATAAAGATATCTATTCAAATTTTATTCGATCTTAATACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.40%	4.60%	0.97%	3.07%	NA
All Indica	2759	90.90%	7.50%	1.34%	0.18%	NA
All Japonica	1512	93.30%	0.30%	0.00%	6.42%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.50%	0.20%	1.34%	0.00%	NA
Indica II	465	84.30%	12.70%	2.80%	0.22%	NA
Indica III	913	88.70%	10.30%	0.88%	0.11%	NA
Indica Intermediate	786	91.70%	6.90%	1.02%	0.38%	NA
Temperate Japonica	767	98.30%	0.50%	0.00%	1.17%	NA
Tropical Japonica	504	98.00%	0.00%	0.00%	1.98%	NA
Japonica Intermediate	241	67.20%	0.40%	0.00%	32.37%	NA
VI/Aromatic	96	55.20%	0.00%	6.25%	38.54%	NA
Intermediate	90	86.70%	4.40%	2.22%	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
vg0620500908	C -> T	LOC_Os06g35165.1	downstream_gene_variant ; 2455.0bp to feature; MODIFIER	silent_mutation	Average:66.516; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N
vg0620500908	C -> T	LOC_Os06g35170.1	downstream_gene_variant ; 957.0bp to feature; MODIFIER	silent_mutation	Average:66.516; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N
vg0620500908	C -> T	LOC_Os06g35165-LOC_Os06g35170	intergenic_region ; MODIFIER	silent_mutation	Average:66.516; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N
vg0620500908	C -> DEL	N	N	silent_mutation	Average:66.516; most accessible tissue: Minghui63 root, score: 81.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620500908	4.01E-06	NA	mr1062_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
vg0620500908	NA	5.62E-07	mr1525_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