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Detailed information for vg0716100570:

Variant ID: vg0716100570 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16100570
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

AGCAGTTAGTAGGCTTGCGTGTGTGTTCTTCTCGTTTGTTTTTCTGCTAGAGTCGTATGGGGCATGGTTATGCCGGTGTGTGGTATAACTGTGTCGGAGC[T/C]
TGTCTTTATTTTATTTGCTTAAGCAACTTGAACTTTAATGAACCAATTTAATAGCAGTAATAAATTCAAGAATTATGGTAGTCGTGGGTGGTTAGTTTTA

Reverse complement sequence

TAAAACTAACCACCCACGACTACCATAATTCTTGAATTTATTACTGCTATTAAATTGGTTCATTAAAGTTCAAGTTGCTTAAGCAAATAAAATAAAGACA[A/G]
GCTCCGACACAGTTATACCACACACCGGCATAACCATGCCCCATACGACTCTAGCAGAAAAACAAACGAGAAGAACACACACGCAAGCCTACTAACTGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.30%	0.30%	24.42%	9.01%	NA
All Indica	2759	51.10%	0.40%	33.78%	14.64%	NA
All Japonica	1512	88.80%	0.00%	11.11%	0.07%	NA
Aus	269	81.00%	0.00%	13.01%	5.95%	NA
Indica I	595	55.50%	0.20%	14.12%	30.25%	NA
Indica II	465	23.90%	0.90%	68.39%	6.88%	NA
Indica III	913	58.30%	0.20%	32.53%	8.98%	NA
Indica Intermediate	786	55.70%	0.60%	29.64%	13.99%	NA
Temperate Japonica	767	79.80%	0.00%	20.21%	0.00%	NA
Tropical Japonica	504	98.20%	0.00%	1.59%	0.20%	NA
Japonica Intermediate	241	97.90%	0.00%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	1.10%	21.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716100570	T -> DEL	N	N	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0716100570	T -> C	LOC_Os07g27560.1	upstream_gene_variant ; 652.0bp to feature; MODIFIER	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0716100570	T -> C	LOC_Os07g27540.1	downstream_gene_variant ; 4688.0bp to feature; MODIFIER	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0716100570	T -> C	LOC_Os07g27550.1	downstream_gene_variant ; 107.0bp to feature; MODIFIER	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0716100570	T -> C	LOC_Os07g27570.1	downstream_gene_variant ; 4056.0bp to feature; MODIFIER	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0716100570	T -> C	LOC_Os07g27550-LOC_Os07g27560	intergenic_region ; MODIFIER	silent_mutation	Average:26.694; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716100570	1.68E-06	NA	mr1265_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
vg0716100570	4.38E-06	4.38E-06	mr1265_2	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
vg0716100570	1.25E-06	1.25E-06	mr1528_2	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