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Detailed information for vg0609207468:

Variant ID: vg0609207468 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 9207468
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.27, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATTTAAATGGTTTGCAGACAAATGATGGGAGCCATGTTTGGATAATAGGTTTGGGATATGATTTCCCATCCTTGAAAGGATAAGTTTCAATTTTAGC[T/C]
ATCCATTCTTCTCACTCCATTTCATCATGTTCCTCCATTCATTTCCATTTTCCAATCCCACCTCTCGTAACTCATTATCCAAACACACCCTTAAGGTTTA

Reverse complement sequence

TAAACCTTAAGGGTGTGTTTGGATAATGAGTTACGAGAGGTGGGATTGGAAAATGGAAATGAATGGAGGAACATGATGAAATGGAGTGAGAAGAATGGAT[A/G]
GCTAAAATTGAAACTTATCCTTTCAAGGATGGGAAATCATATCCCAAACCTATTATCCAAACATGGCTCCCATCATTTGTCTGCAAACCATTTAAATAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.90%	13.00%	0.04%	0.00%	NA
All Indica	2759	87.40%	12.60%	0.00%	0.00%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.00%	NA
Aus	269	7.40%	92.20%	0.37%	0.00%	NA
Indica I	595	95.60%	4.40%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	79.50%	20.50%	0.00%	0.00%	NA
Indica Intermediate	786	83.30%	16.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0609207468	T -> C	LOC_Os06g16160.1	upstream_gene_variant ; 1002.0bp to feature; MODIFIER	silent_mutation	Average:56.25; most accessible tissue: Minghui63 root, score: 86.877	N	N	N	N
vg0609207468	T -> C	LOC_Os06g16170.1	downstream_gene_variant ; 282.0bp to feature; MODIFIER	silent_mutation	Average:56.25; most accessible tissue: Minghui63 root, score: 86.877	N	N	N	N
vg0609207468	T -> C	LOC_Os06g16160-LOC_Os06g16170	intergenic_region ; MODIFIER	silent_mutation	Average:56.25; most accessible tissue: Minghui63 root, score: 86.877	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0609207468	NA	3.71E-20	mr1244	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
vg0609207468	NA	7.35E-14	mr1874	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
vg0609207468	NA	2.31E-08	mr1068_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
vg0609207468	8.23E-06	2.41E-11	mr1087_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
vg0609207468	NA	7.24E-07	mr1090_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
vg0609207468	6.03E-06	NA	mr1091_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
vg0609207468	2.40E-06	NA	mr1108_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
vg0609207468	1.52E-06	NA	mr1112_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
vg0609207468	4.03E-07	NA	mr1234_2	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
vg0609207468	4.52E-06	NA	mr1234_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
vg0609207468	NA	9.83E-18	mr1240_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
vg0609207468	8.59E-06	1.71E-07	mr1570_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
vg0609207468	NA	2.41E-12	mr1803_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
vg0609207468	NA	7.57E-15	mr1961_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