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Detailed information for vg0114563958:

Variant ID: vg0114563958 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14563958
Reference Allele: T	Alternative Allele: A,G
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATACTAGCCTCTCCCAGAAGAGCGTGGAATGCTGGTGGGTACGGCGGGGTGAGGAAGAAGTAGCGGTCACGGCCTACTGCTGTGGAAGTAGAAGCCCCTG[T/A,G]
AGTGCTGATCTTGGCTGCTCAAAGCTGCTCCTCCAGCTGGCTGATGTGCTCCTGACTCTCTCTCAGCTGCTCCTCCAGAGTATCCATCATCCCGCGGCGA

Reverse complement sequence

TCGCCGCGGGATGATGGATACTCTGGAGGAGCAGCTGAGAGAGAGTCAGGAGCACATCAGCCAGCTGGAGGAGCAGCTTTGAGCAGCCAAGATCAGCACT[A/T,C]
CAGGGGCTTCTACTTCCACAGCAGTAGGCCGTGACCGCTACTTCTTCCTCACCCCGCCGTACCCACCAGCATTCCACGCTCTTCTGGGAGAGGCTAGTAT

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	53.00%	0.60%	11.00%	35.38%	G: 0.04%
All Indica	2759	42.40%	0.90%	13.70%	42.91%	G: 0.07%
All Japonica	1512	68.40%	0.00%	4.83%	26.79%	NA
Aus	269	54.60%	1.10%	22.68%	21.56%	NA
Indica I	595	25.90%	2.00%	8.91%	63.19%	NA
Indica II	465	45.20%	0.00%	13.33%	41.51%	NA
Indica III	913	50.70%	0.90%	16.98%	31.33%	G: 0.11%
Indica Intermediate	786	43.60%	0.60%	13.74%	41.86%	G: 0.13%
Temperate Japonica	767	90.50%	0.00%	0.39%	9.13%	NA
Tropical Japonica	504	39.90%	0.00%	9.13%	50.99%	NA
Japonica Intermediate	241	57.70%	0.00%	9.96%	32.37%	NA
VI/Aromatic	96	93.80%	0.00%	3.12%	3.12%	NA
Intermediate	90	70.00%	0.00%	5.56%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114563958	T -> G	LOC_Os01g25679.1	upstream_gene_variant ; 3983.0bp to feature; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> G	LOC_Os01g25700.1	downstream_gene_variant ; 3263.0bp to feature; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> G	LOC_Os01g25688.1	intron_variant ; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> A	LOC_Os01g25679.1	upstream_gene_variant ; 3983.0bp to feature; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> A	LOC_Os01g25700.1	downstream_gene_variant ; 3263.0bp to feature; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> A	LOC_Os01g25688.1	intron_variant ; MODIFIER	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N
vg0114563958	T -> DEL	N	N	silent_mutation	Average:15.087; most accessible tissue: Callus, score: 31.809	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114563958	6.95E-07	NA	mr1870	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