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Detailed information for vg0413093616:

Variant ID: vg0413093616 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13093616
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: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AACGACGGTGGTGTGACCAACCAACCGTATAGGCGAAGACACCAGTCGGTGGCGACGACGGCAAGCCGGTGGTGATGTTCTGACTGATCCATTCCTGGAG[T/C]
GTAAGAGATAAGCTTAAAGCCATGAATCCCTTTTATGCGTATTTGGATCTGGATCCTGCAGAACAAACATATAGGATGAGTAGTATCTGATGTACATATA

Reverse complement sequence

TATATGTACATCAGATACTACTCATCCTATATGTTTGTTCTGCAGGATCCAGATCCAAATACGCATAAAAGGGATTCATGGCTTTAAGCTTATCTCTTAC[A/G]
CTCCAGGAATGGATCAGTCAGAACATCACCACCGGCTTGCCGTCGTCGCCACCGACTGGTGTCTTCGCCTATACGGTTGGTTGGTCACACCACCGTCGTT

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	42.30%	39.50%	1.14%	16.99%	NA
All Indica	2759	68.20%	10.70%	1.45%	19.64%	NA
All Japonica	1512	5.40%	94.00%	0.33%	0.33%	NA
Aus	269	1.90%	7.10%	3.35%	87.73%	NA
Indica I	595	61.70%	26.40%	0.84%	11.09%	NA
Indica II	465	72.00%	9.70%	3.44%	14.84%	NA
Indica III	913	67.60%	2.80%	1.10%	28.48%	NA
Indica Intermediate	786	71.60%	8.50%	1.15%	18.70%	NA
Temperate Japonica	767	3.50%	95.80%	0.65%	0.00%	NA
Tropical Japonica	504	1.20%	98.00%	0.00%	0.79%	NA
Japonica Intermediate	241	19.90%	79.70%	0.00%	0.41%	NA
VI/Aromatic	96	0.00%	90.60%	0.00%	9.38%	NA
Intermediate	90	35.60%	52.20%	0.00%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0413093616	T -> C	LOC_Os04g23040.1	upstream_gene_variant ; 4611.0bp to feature; MODIFIER	silent_mutation	Average:22.694; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0413093616	T -> C	LOC_Os04g23060.1	upstream_gene_variant ; 2617.0bp to feature; MODIFIER	silent_mutation	Average:22.694; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0413093616	T -> C	LOC_Os04g23050.1	downstream_gene_variant ; 1584.0bp to feature; MODIFIER	silent_mutation	Average:22.694; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0413093616	T -> C	LOC_Os04g23050-LOC_Os04g23060	intergenic_region ; MODIFIER	silent_mutation	Average:22.694; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N
vg0413093616	T -> DEL	N	N	silent_mutation	Average:22.694; most accessible tissue: Minghui63 flag leaf, score: 52.88	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413093616	1.23E-08	1.63E-08	mr1546_2	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