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Detailed information for vg0412756324:

Variant ID: vg0412756324 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12756324
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAAGGATTTTAATTTTAATTCTATGGCATCACTAATGGCGTCATTTCCTATATCATTTCTACCGTATGGTGATTTGATTTGGGATTTTAAATTATTTAC[A/T]
TTATCACTTCTAACCTTTGGTGATGTGACTTAAGACATTAATGTTTATTCCCTAATCAGTTCTGCCCAACGGTGATTTGATTTTTGGATTATAAGTAATT

Reverse complement sequence

AATTACTTATAATCCAAAAATCAAATCACCGTTGGGCAGAACTGATTAGGGAATAAACATTAATGTCTTAAGTCACATCACCAAAGGTTAGAAGTGATAA[T/A]
GTAAATAATTTAAAATCCCAAATCAAATCACCATACGGTAGAAATGATATAGGAAATGACGCCATTAGTGATGCCATAGAATTAAAATTAAAATCCTTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.30%	0.60%	0.19%	62.87%	NA
All Indica	2759	3.40%	1.00%	0.22%	95.32%	NA
All Japonica	1512	98.20%	0.00%	0.13%	1.65%	NA
Aus	269	0.70%	0.00%	0.00%	99.26%	NA
Indica I	595	3.70%	0.20%	0.34%	95.80%	NA
Indica II	465	4.30%	4.30%	0.22%	91.18%	NA
Indica III	913	1.90%	0.10%	0.00%	98.03%	NA
Indica Intermediate	786	4.60%	0.80%	0.38%	94.27%	NA
Temperate Japonica	767	98.40%	0.00%	0.26%	1.30%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	96.30%	0.00%	0.00%	3.73%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	55.60%	1.10%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412756324	A -> DEL	N	N	silent_mutation	Average:14.827; most accessible tissue: Callus, score: 40.121	N	N	N	N
vg0412756324	A -> T	LOC_Os04g22520.1	upstream_gene_variant ; 4642.0bp to feature; MODIFIER	silent_mutation	Average:14.827; most accessible tissue: Callus, score: 40.121	N	N	N	N
vg0412756324	A -> T	LOC_Os04g22510-LOC_Os04g22520	intergenic_region ; MODIFIER	silent_mutation	Average:14.827; most accessible tissue: Callus, score: 40.121	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412756324	2.88E-06	NA	mr1844	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
vg0412756324	NA	9.52E-08	mr1212_2	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