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Detailed information for vg1214302244:

Variant ID: vg1214302244 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14302244
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATACAGAGCCAAGTCCCGAAATGTGTAGTCAAGCAGGGTATACGGCAGAGAATCCCCTTTCAACGGATCGTTTTACCGAAAATATGAAAGCGAAGTAGT[T/G]
ATGACCAGAGAACAAAAACTCTCGGCAGCATCAAAGTCAGCTTCTGGCAGTCGCGCAGATTACAATATTTTTGGGAAAGCAGTTGCATGGTTTGCAGTTC

Reverse complement sequence

GAACTGCAAACCATGCAACTGCTTTCCCAAAAATATTGTAATCTGCGCGACTGCCAGAAGCTGACTTTGATGCTGCCGAGAGTTTTTGTTCTCTGGTCAT[A/C]
ACTACTTCGCTTTCATATTTTCGGTAAAACGATCCGTTGAAAGGGGATTCTCTGCCGTATACCCTGCTTGACTACACATTTCGGGACTTGGCTCTGTATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.80%	10.20%	8.80%	6.22%	NA
All Indica	2759	58.90%	17.00%	14.61%	9.46%	NA
All Japonica	1512	97.90%	0.30%	0.26%	1.52%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	47.40%	23.50%	25.04%	4.03%	NA
Indica II	465	65.60%	3.70%	10.97%	19.78%	NA
Indica III	913	63.60%	17.60%	11.72%	7.01%	NA
Indica Intermediate	786	58.30%	19.20%	12.21%	10.31%	NA
Temperate Japonica	767	96.30%	0.70%	0.26%	2.74%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.41%	0.83%	NA
VI/Aromatic	96	81.20%	7.30%	5.21%	6.25%	NA
Intermediate	90	90.00%	1.10%	4.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214302244	T -> DEL	N	N	silent_mutation	Average:26.861; most accessible tissue: Zhenshan97 young leaf, score: 39.843	N	N	N	N
vg1214302244	T -> G	LOC_Os12g24910.1	downstream_gene_variant ; 831.0bp to feature; MODIFIER	silent_mutation	Average:26.861; most accessible tissue: Zhenshan97 young leaf, score: 39.843	N	N	N	N
vg1214302244	T -> G	LOC_Os12g24910-LOC_Os12g24920	intergenic_region ; MODIFIER	silent_mutation	Average:26.861; most accessible tissue: Zhenshan97 young leaf, score: 39.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214302244	7.34E-06	7.40E-06	mr1708	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