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Detailed information for vg0608390668:

Variant ID: vg0608390668 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8390668
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

ATTACTCTTATTCATGATAATCACACCAGTACAATATTTGGGGTAGCCTATCTAACTGTTGTCGACATGGCGGTCTGACGATCTGACTCGTAGTCGACAA[C/T]
AGGGTAGCCTTCCTCCTCGAATCCGTGCCCGGCGAGATAAGAGATAGCGCTTTCGTCTCTCCTGACAGTATCCGGAGACACCGTAGGGTACTAGCCATGC

Reverse complement sequence

GCATGGCTAGTACCCTACGGTGTCTCCGGATACTGTCAGGAGAGACGAAAGCGCTATCTCTTATCTCGCCGGGCACGGATTCGAGGAGGAAGGCTACCCT[G/A]
TTGTCGACTACGAGTCAGATCGTCAGACCGCCATGTCGACAACAGTTAGATAGGCTACCCCAAATATTGTACTGGTGTGATTATCATGAATAAGAGTAAT

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	74.90%	18.60%	4.95%	1.52%	NA
All Indica	2759	66.50%	22.70%	8.26%	2.61%	NA
All Japonica	1512	99.70%	0.30%	0.07%	0.00%	NA
Aus	269	10.40%	88.50%	1.12%	0.00%	NA
Indica I	595	61.20%	27.70%	8.91%	2.18%	NA
Indica II	465	84.50%	13.50%	1.72%	0.22%	NA
Indica III	913	52.60%	28.30%	14.13%	5.04%	NA
Indica Intermediate	786	76.00%	17.70%	4.83%	1.53%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	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
vg0608390668	C -> T	LOC_Os06g14790.1	upstream_gene_variant ; 326.0bp to feature; MODIFIER	silent_mutation	Average:36.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0608390668	C -> T	LOC_Os06g14800.1	upstream_gene_variant ; 4218.0bp to feature; MODIFIER	silent_mutation	Average:36.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0608390668	C -> T	LOC_Os06g14790-LOC_Os06g14800	intergenic_region ; MODIFIER	silent_mutation	Average:36.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0608390668	C -> DEL	N	N	silent_mutation	Average:36.893; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608390668	3.03E-06	1.30E-08	mr1570_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