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Detailed information for vg0716934852:

Variant ID: vg0716934852 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16934852
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAATAAATAATATTTACATAATATTTTTAATAAGACGAATAGTTAAACGGTATAAAAAATTCGGTGACACGAAGGGAGTAATATATATGGTTCATCGC[C/T]
AGTGATCGAGCGATGCACGCACTGATGATCTGATCATATACGTGTTGCATTCACACGCAGGTGAAGACGAGCAGCAGCGGCGGTGGCGGGAAGGAGGGGA

Reverse complement sequence

TCCCCTCCTTCCCGCCACCGCCGCTGCTGCTCGTCTTCACCTGCGTGTGAATGCAACACGTATATGATCAGATCATCAGTGCGTGCATCGCTCGATCACT[G/A]
GCGATGAACCATATATATTACTCCCTTCGTGTCACCGAATTTTTTATACCGTTTAACTATTCGTCTTATTAAAAATATTATGTAAATATTATTTATTTTG

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	79.10%	17.80%	3.15%	0.00%	NA
All Indica	2759	97.70%	2.10%	0.18%	0.00%	NA
All Japonica	1512	48.40%	42.50%	9.06%	0.00%	NA
Aus	269	88.10%	11.90%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	99.00%	0.80%	0.22%	0.00%	NA
Indica Intermediate	786	94.10%	5.60%	0.25%	0.00%	NA
Temperate Japonica	767	68.70%	22.40%	8.87%	0.00%	NA
Tropical Japonica	504	27.20%	65.70%	7.14%	0.00%	NA
Japonica Intermediate	241	28.20%	58.10%	13.69%	0.00%	NA
VI/Aromatic	96	7.30%	89.60%	3.12%	0.00%	NA
Intermediate	90	71.10%	24.40%	4.44%	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
vg0716934852	C -> T	LOC_Os07g28880.1	upstream_gene_variant ; 2219.0bp to feature; MODIFIER	silent_mutation	Average:59.815; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N
vg0716934852	C -> T	LOC_Os07g28890.1	intron_variant ; MODIFIER	silent_mutation	Average:59.815; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716934852	2.44E-10	NA	mr1238	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
vg0716934852	2.39E-09	NA	mr1309	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
vg0716934852	NA	7.71E-06	mr1398	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
vg0716934852	4.20E-06	NA	mr1484	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
vg0716934852	NA	9.12E-09	mr1554	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
vg0716934852	NA	6.09E-06	mr1602	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
vg0716934852	1.17E-07	NA	mr1841	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
vg0716934852	8.59E-08	4.55E-15	mr1900	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
vg0716934852	NA	1.44E-07	mr1900	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