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Detailed information for vg0608860852:

Variant ID: vg0608860852 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8860852
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

ACTAGATCCATATGAATCCGCCTGACATCCCGAAGACAGCCTTCATCACCCCGTTCGGCACTTTCTGTCACCTCAGGATGCCTTTCGGCCTAAGGAATGC[C/T]
GGAGCAACCTTTGCCAGACTGGTATACAAAGTCCTTTGCAACCAGCTGGGGCGAAATGTAGAAGCTTATGTCGACGATATTGTCGTGAAAAGCCGTAGGG

Reverse complement sequence

CCCTACGGCTTTTCACGACAATATCGTCGACATAAGCTTCTACATTTCGCCCCAGCTGGTTGCAAAGGACTTTGTATACCAGTCTGGCAAAGGTTGCTCC[G/A]
GCATTCCTTAGGCCGAAAGGCATCCTGAGGTGACAGAAAGTGCCGAACGGGGTGATGAAGGCTGTCTTCGGGATGTCAGGCGGATTCATATGGATCTAGT

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	63.30%	6.70%	6.81%	23.21%	NA
All Indica	2759	71.60%	5.50%	8.34%	14.57%	NA
All Japonica	1512	43.30%	10.50%	4.43%	41.80%	NA
Aus	269	97.80%	0.00%	1.12%	1.12%	NA
Indica I	595	70.60%	0.70%	4.54%	24.20%	NA
Indica II	465	73.30%	2.80%	9.89%	13.98%	NA
Indica III	913	70.50%	11.70%	10.41%	7.34%	NA
Indica Intermediate	786	72.50%	3.60%	7.89%	16.03%	NA
Temperate Japonica	767	74.40%	0.00%	2.35%	23.21%	NA
Tropical Japonica	504	9.30%	28.20%	6.94%	55.56%	NA
Japonica Intermediate	241	14.90%	7.10%	5.81%	72.20%	NA
VI/Aromatic	96	39.60%	0.00%	12.50%	47.92%	NA
Intermediate	90	68.90%	4.40%	11.11%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608860852	C -> T	LOC_Os06g15640.1	synonymous_variant ; p.Ala611Ala; LOW	synonymous_codon	Average:32.582; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0608860852	C -> DEL	LOC_Os06g15640.1	N	frameshift_variant	Average:32.582; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608860852	4.95E-06	4.95E-06	mr1131_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
vg0608860852	1.65E-06	5.15E-09	mr1653_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
vg0608860852	4.88E-06	NA	mr1668_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