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Detailed information for vg0713573114:

Variant ID: vg0713573114 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13573114
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTGTTTCACATAGGACGAGGACATGGCATCCTATTACCAGCCATCACATGAAATTAATAGGATATGCCACGTCATCATCCTAAATGGAATAACCACGT[C/T]
ATCACACGGGTGAATCCATTCATCCATAGTGTGGTTTTGTGAAACTAAACTAACAAAATATATGTATTTAAGTGTAAAGTGTTAAAATGCGTGTGGTTTT

Reverse complement sequence

AAAACCACACGCATTTTAACACTTTACACTTAAATACATATATTTTGTTAGTTTAGTTTCACAAAACCACACTATGGATGAATGGATTCACCCGTGTGAT[G/A]
ACGTGGTTATTCCATTTAGGATGATGACGTGGCATATCCTATTAATTTCATGTGATGGCTGGTAATAGGATGCCATGTCCTCGTCCTATGTGAAACAGCC

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	37.00%	22.10%	1.93%	38.93%	NA
All Indica	2759	4.30%	30.00%	2.07%	63.54%	NA
All Japonica	1512	98.40%	0.90%	0.00%	0.66%	NA
Aus	269	5.60%	64.30%	12.27%	17.84%	NA
Indica I	595	0.80%	28.90%	0.67%	69.58%	NA
Indica II	465	3.90%	15.30%	1.51%	79.35%	NA
Indica III	913	2.20%	36.90%	3.50%	57.39%	NA
Indica Intermediate	786	9.80%	31.70%	1.78%	56.74%	NA
Temperate Japonica	767	98.60%	0.70%	0.00%	0.78%	NA
Tropical Japonica	504	99.20%	0.40%	0.00%	0.40%	NA
Japonica Intermediate	241	96.30%	2.90%	0.00%	0.83%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	50.00%	16.70%	1.11%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713573114	C -> DEL	N	N	silent_mutation	Average:57.474; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0713573114	C -> T	LOC_Os07g23980.1	upstream_gene_variant ; 354.0bp to feature; MODIFIER	silent_mutation	Average:57.474; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N
vg0713573114	C -> T	LOC_Os07g23970-LOC_Os07g23980	intergenic_region ; MODIFIER	silent_mutation	Average:57.474; most accessible tissue: Minghui63 root, score: 77.29	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713573114	2.91E-06	NA	mr1528	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
vg0713573114	NA	2.26E-06	mr1380_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
vg0713573114	NA	2.83E-06	mr1561_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
vg0713573114	NA	6.76E-07	mr1875_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
vg0713573114	NA	1.66E-06	mr1908_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
vg0713573114	NA	3.19E-06	mr1996_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