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Detailed information for vg0322718664:

Variant ID: vg0322718664 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22718664
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: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TGAATCTCAGCAAGATAATCTCAACCGTTGAGTGATGAATGAAAGAATGAAGGAATGATTGAAACCATTTGTTGAACTATAGGGTAGAAGATCATTCGTC[C/T]
AGTATTTCTTAAAATAAAATCTTCAATTATATCTTCATAATTAATCATGTCCAAGATATCATTTTCAAGTGCTATTGTTGCAAGCAGCAAGCTATATCAC

Reverse complement sequence

GTGATATAGCTTGCTGCTTGCAACAATAGCACTTGAAAATGATATCTTGGACATGATTAATTATGAAGATATAATTGAAGATTTTATTTTAAGAAATACT[G/A]
GACGAATGATCTTCTACCCTATAGTTCAACAAATGGTTTCAATCATTCCTTCATTCTTTCATTCATCACTCAACGGTTGAGATTATCTTGCTGAGATTCA

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	40.80%	0.30%	0.32%	58.63%	NA
All Indica	2759	2.50%	0.40%	0.36%	96.74%	NA
All Japonica	1512	99.30%	0.00%	0.07%	0.60%	NA
Aus	269	84.40%	0.40%	0.00%	15.24%	NA
Indica I	595	0.80%	0.30%	0.84%	97.98%	NA
Indica II	465	1.50%	0.20%	0.22%	98.06%	NA
Indica III	913	1.20%	0.30%	0.22%	98.25%	NA
Indica Intermediate	786	5.90%	0.60%	0.25%	93.26%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	98.60%	0.00%	0.00%	1.39%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	81.20%	1.00%	4.17%	13.54%	NA
Intermediate	90	56.70%	0.00%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0322718664	C -> T	LOC_Os03g40870.1	upstream_gene_variant ; 4349.0bp to feature; MODIFIER	silent_mutation	Average:70.505; most accessible tissue: Callus, score: 93.738	N	N	N	N
vg0322718664	C -> T	LOC_Os03g40860.1	downstream_gene_variant ; 3257.0bp to feature; MODIFIER	silent_mutation	Average:70.505; most accessible tissue: Callus, score: 93.738	N	N	N	N
vg0322718664	C -> T	LOC_Os03g40840-LOC_Os03g40860	intergenic_region ; MODIFIER	silent_mutation	Average:70.505; most accessible tissue: Callus, score: 93.738	N	N	N	N
vg0322718664	C -> DEL	N	N	silent_mutation	Average:70.505; most accessible tissue: Callus, score: 93.738	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322718664	NA	3.64E-11	mr1657	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
vg0322718664	NA	1.12E-07	mr1750	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
vg0322718664	4.13E-08	2.29E-14	mr1750_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