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Detailed information for vg1224673904:

Variant ID: vg1224673904 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24673904
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAAAATCGGGTGCCCACGTCATGCTGACGTCAGCATGATGCATGCGTGCAAAATCACTTTAAACTAATTTTTGTCTTAAATTATTTATCTAAATTATGA[T/A]
CCGATTGCACCATTAAATTCGTTACAATTAAATCTTTAAAACAAAACCACACATGGATATATTCCGACGAAAATTTTTTTAGCTTATTATTGAATTATTT

Reverse complement sequence

AAATAATTCAATAATAAGCTAAAAAAATTTTCGTCGGAATATATCCATGTGTGGTTTTGTTTTAAAGATTTAATTGTAACGAATTTAATGGTGCAATCGG[A/T]
TCATAATTTAGATAAATAATTTAAGACAAAAATTAGTTTAAAGTGATTTTGCACGCATGCATCATGCTGACGTCAGCATGACGTGGGCACCCGATTTTCC

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	90.00%	9.60%	0.11%	0.30%	NA
All Indica	2759	99.40%	0.10%	0.00%	0.51%	NA
All Japonica	1512	75.10%	24.60%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.60%	0.00%	0.00%	1.42%	NA
Indica Intermediate	786	99.60%	0.30%	0.00%	0.13%	NA
Temperate Japonica	767	85.80%	14.00%	0.26%	0.00%	NA
Tropical Japonica	504	74.60%	25.00%	0.40%	0.00%	NA
Japonica Intermediate	241	41.90%	57.70%	0.41%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg1224673904	T -> DEL	N	N	silent_mutation	Average:34.519; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1224673904	T -> A	LOC_Os12g39920.1	upstream_gene_variant ; 2288.0bp to feature; MODIFIER	silent_mutation	Average:34.519; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N
vg1224673904	T -> A	LOC_Os12g39920-LOC_Os12g39930	intergenic_region ; MODIFIER	silent_mutation	Average:34.519; most accessible tissue: Zhenshan97 panicle, score: 57.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224673904	2.75E-06	NA	mr1648	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