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Detailed information for vg0513252916:

Variant ID: vg0513252916 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 13252916
Reference Allele: T	Alternative Allele: A,C
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAAACATAGCTCCAAAAGTAATATAACAACAAAAAACATTGGAGGATGAAGTTACTAACCTTTTAGACACCTCCGATTTGTATATAATCACTAAAAAAA[T/A,C]
TCCACAAGAAATTTGGGCATGACCTCCCCTCTTTCTTTGAGAAATTTTGAAGGTTGCTCGGGCTGGAGGAGGAAGAAGACATATATAAAGGGGTGGATCT

Reverse complement sequence

AGATCCACCCCTTTATATATGTCTTCTTCCTCCTCCAGCCCGAGCAACCTTCAAAATTTCTCAAAGAAAGAGGGGAGGTCATGCCCAAATTTCTTGTGGA[A/T,G]
TTTTTTTAGTGATTATATACAAATCGGAGGTGTCTAAAAGGTTAGTAACTTCATCCTCCAATGTTTTTTGTTGTTATATTACTTTTGGAGCTATGTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	2.40%	0.28%	0.23%	NA
All Indica	2759	95.40%	4.10%	0.47%	0.00%	NA
All Japonica	1512	99.30%	0.00%	0.00%	0.73%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.40%	6.10%	0.50%	0.00%	NA
Indica II	465	94.00%	4.70%	1.29%	0.00%	NA
Indica III	913	97.80%	2.10%	0.11%	0.00%	NA
Indica Intermediate	786	94.90%	4.70%	0.38%	0.00%	NA
Temperate Japonica	767	98.60%	0.00%	0.00%	1.43%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0513252916	T -> DEL	N	N	silent_mutation	Average:33.763; most accessible tissue: Minghui63 flower, score: 42.268	N	N	N	N
vg0513252916	T -> C	LOC_Os05g23210.1	upstream_gene_variant ; 3559.0bp to feature; MODIFIER	N	Average:33.763; most accessible tissue: Minghui63 flower, score: 42.268	N	N	N	N
vg0513252916	T -> C	LOC_Os05g23220.1	intron_variant ; MODIFIER	N	Average:33.763; most accessible tissue: Minghui63 flower, score: 42.268	N	N	N	N
vg0513252916	T -> A	LOC_Os05g23210.1	upstream_gene_variant ; 3559.0bp to feature; MODIFIER	silent_mutation	Average:33.763; most accessible tissue: Minghui63 flower, score: 42.268	N	N	N	N
vg0513252916	T -> A	LOC_Os05g23220.1	intron_variant ; MODIFIER	silent_mutation	Average:33.763; most accessible tissue: Minghui63 flower, score: 42.268	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0513252916	3.38E-06	4.39E-06	mr1256	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