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Detailed information for vg0504497766:

Variant ID: vg0504497766 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 4497766
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCTCGCCAAACAGAGAAGGAAACAGAGAAGGAAGGGATGCTGCGTGCGTGATGCGGAATAGACGCGAAAGTACATAACTACCCTCCCACCCACGGTAC[C/T]
GCTTCAAGGCAGAGGTGCGGTACCATGAGGTACAGATGATTTTTGACCGTCCGATGAGGCCTGATCAACGGTCACGATTTGGTACTGCACAGCCTCAAGG

Reverse complement sequence

CCTTGAGGCTGTGCAGTACCAAATCGTGACCGTTGATCAGGCCTCATCGGACGGTCAAAAATCATCTGTACCTCATGGTACCGCACCTCTGCCTTGAAGC[G/A]
GTACCGTGGGTGGGAGGGTAGTTATGTACTTTCGCGTCTATTCCGCATCACGCACGCAGCATCCCTTCCTTCTCTGTTTCCTTCTCTGTTTGGCGAGAGA

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	51.70%	7.10%	12.38%	28.84%	NA
All Indica	2759	20.40%	12.10%	20.41%	47.08%	NA
All Japonica	1512	97.70%	0.00%	0.46%	1.85%	NA
Aus	269	94.80%	0.00%	1.86%	3.35%	NA
Indica I	595	14.10%	7.90%	12.94%	65.04%	NA
Indica II	465	15.70%	13.10%	16.34%	54.84%	NA
Indica III	913	26.20%	14.90%	28.81%	30.12%	NA
Indica Intermediate	786	21.10%	11.60%	18.70%	48.60%	NA
Temperate Japonica	767	98.60%	0.00%	0.26%	1.17%	NA
Tropical Japonica	504	95.60%	0.00%	0.79%	3.57%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	87.50%	0.00%	4.17%	8.33%	NA
Intermediate	90	70.00%	2.20%	6.67%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0504497766	C -> T	LOC_Os05g08250.1	upstream_gene_variant ; 3268.0bp to feature; MODIFIER	silent_mutation	Average:16.68; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0504497766	C -> T	LOC_Os05g08240.1	intron_variant ; MODIFIER	silent_mutation	Average:16.68; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0504497766	C -> DEL	N	N	silent_mutation	Average:16.68; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0504497766	NA	1.73E-21	mr1020	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
vg0504497766	NA	6.16E-50	mr1109	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
vg0504497766	NA	8.22E-10	mr1301	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
vg0504497766	NA	2.77E-08	mr1410	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
vg0504497766	NA	1.73E-26	mr1877	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
vg0504497766	NA	3.54E-08	mr1929	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
vg0504497766	NA	7.69E-59	mr1109_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
vg0504497766	NA	2.38E-37	mr1129_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
vg0504497766	NA	6.42E-28	mr1270_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
vg0504497766	2.00E-06	NA	mr1301_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
vg0504497766	1.77E-06	NA	mr1410_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
vg0504497766	NA	2.31E-14	mr1720_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
vg0504497766	NA	1.68E-31	mr1913_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
vg0504497766	NA	2.19E-29	mr1932_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
vg0504497766	NA	1.05E-07	mr1993_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