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Detailed information for vg0716582032:

Variant ID: vg0716582032 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16582032
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: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTCTTATTTGTTTGTTTTTTGTGATGTGATGTTGATTTTATCCTTTTGAGTGCTCACCATGTCATATCATTTGCATATCATATCTATTTTTCTTACTG[C/T]
TTATTTGCATCCCACGAATGAGCAGGGATGAAGGAAACTCTCCTCGGTTGCTCCCTTATATATATGCATATGAGTTTCACTCATATCTTCCATATGCATA

Reverse complement sequence

TATGCATATGGAAGATATGAGTGAAACTCATATGCATATATATAAGGGAGCAACCGAGGAGAGTTTCCTTCATCCCTGCTCATTCGTGGGATGCAAATAA[G/A]
CAGTAAGAAAAATAGATATGATATGCAAATGATATGACATGGTGAGCACTCAAAAGGATAAAATCAACATCACATCACAAAAAACAAACAAATAAGACAC

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	66.90%	3.90%	1.52%	27.70%	NA
All Indica	2759	50.70%	0.50%	2.54%	46.28%	NA
All Japonica	1512	99.50%	0.10%	0.00%	0.46%	NA
Aus	269	37.50%	62.50%	0.00%	0.00%	NA
Indica I	595	72.10%	0.20%	0.50%	27.23%	NA
Indica II	465	20.60%	0.20%	2.58%	76.56%	NA
Indica III	913	45.20%	0.00%	4.16%	50.60%	NA
Indica Intermediate	786	58.70%	1.40%	2.16%	37.79%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	0.00%	2.22%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716582032	C -> DEL	N	N	silent_mutation	Average:20.134; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0716582032	C -> T	LOC_Os07g28370.1	downstream_gene_variant ; 447.0bp to feature; MODIFIER	silent_mutation	Average:20.134; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N
vg0716582032	C -> T	LOC_Os07g28370-LOC_Os07g28380	intergenic_region ; MODIFIER	silent_mutation	Average:20.134; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716582032	NA	3.88E-41	mr1549	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
vg0716582032	1.24E-08	4.37E-53	mr1550	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
vg0716582032	2.63E-06	5.90E-47	mr1757	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
vg0716582032	8.64E-08	1.22E-40	mr1549_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
vg0716582032	4.14E-12	1.52E-64	mr1550_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
vg0716582032	1.62E-06	9.38E-35	mr1757_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