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Detailed information for vg0716242048:

Variant ID: vg0716242048 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16242048
Reference Allele: T	Alternative Allele: C
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTACAATCTAACTCAGCGCCTATTACAGCAGTCTTATCAGGATCGGAGGGATCTAAGGGAATTTTTTTCGTCTTGGCATCACTTTCTTCGGTCTTCGT[T/C]
AGCTTGGTTGCGGGCACTTCTCCCTCGCTTGCTGTGGTCGCAGCCAGTCGGACCTCTTCGCGGGCGAGCGTAGTCTCGTGGGTTTGGGCCATCTCGCAAC

Reverse complement sequence

GTTGCGAGATGGCCCAAACCCACGAGACTACGCTCGCCCGCGAAGAGGTCCGACTGGCTGCGACCACAGCAAGCGAGGGAGAAGTGCCCGCAACCAAGCT[A/G]
ACGAAGACCGAAGAAAGTGATGCCAAGACGAAAAAAATTCCCTTAGATCCCTCCGATCCTGATAAGACTGCTGTAATAGGCGCTGAGTTAGATTGTAAAT

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	35.20%	25.60%	38.89%	0.23%	NA
All Indica	2759	30.90%	4.10%	64.66%	0.40%	NA
All Japonica	1512	35.50%	63.20%	1.26%	0.00%	NA
Aus	269	87.70%	11.90%	0.37%	0.00%	NA
Indica I	595	44.50%	1.70%	53.11%	0.67%	NA
Indica II	465	18.10%	3.00%	78.49%	0.43%	NA
Indica III	913	22.80%	3.20%	73.71%	0.33%	NA
Indica Intermediate	786	37.50%	7.50%	54.71%	0.25%	NA
Temperate Japonica	767	20.50%	77.80%	1.69%	0.00%	NA
Tropical Japonica	504	64.90%	34.50%	0.60%	0.00%	NA
Japonica Intermediate	241	22.00%	76.80%	1.24%	0.00%	NA
VI/Aromatic	96	15.60%	84.40%	0.00%	0.00%	NA
Intermediate	90	27.80%	34.40%	37.78%	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
vg0716242048	T -> DEL	N	N	silent_mutation	Average:8.747; most accessible tissue: Callus, score: 30.671	N	N	N	N
vg0716242048	T -> C	LOC_Os07g27820.1	downstream_gene_variant ; 3595.0bp to feature; MODIFIER	silent_mutation	Average:8.747; most accessible tissue: Callus, score: 30.671	N	N	N	N
vg0716242048	T -> C	LOC_Os07g27834.1	intron_variant ; MODIFIER	silent_mutation	Average:8.747; most accessible tissue: Callus, score: 30.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716242048	NA	5.80E-08	mr1800	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
vg0716242048	2.30E-06	2.30E-06	mr1899	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
vg0716242048	8.47E-06	8.47E-06	mr1954	Jap_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
vg0716242048	NA	1.07E-06	mr1977	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