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Detailed information for vg1219758226:

Variant ID: vg1219758226 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19758226
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTATTCAAAAATTTTATACAAATGTATATGATATAAATCACACTTAAAGTACTATGAGTGATAAAACAACTCATAACAAAATAAATTATAATTACGTA[A/G]
ATTTTTTGAATAAGACGAATGGTCAAACATATGAGAAAAAGTCAACAGCGTCATCTATTAAAAAACGGAGGTAGTATTAATTAATGGCAGCTTGGCCGTG

Reverse complement sequence

CACGGCCAAGCTGCCATTAATTAATACTACCTCCGTTTTTTAATAGATGACGCTGTTGACTTTTTCTCATATGTTTGACCATTCGTCTTATTCAAAAAAT[T/C]
TACGTAATTATAATTTATTTTGTTATGAGTTGTTTTATCACTCATAGTACTTTAAGTGTGATTTATATCATATACATTTGTATAAAATTTTTGAATAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.10%	4.10%	1.59%	0.25%	NA
All Indica	2759	99.60%	0.00%	0.40%	0.00%	NA
All Japonica	1512	87.20%	12.40%	0.33%	0.00%	NA
Aus	269	74.30%	0.00%	21.19%	4.46%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	99.70%	0.00%	0.33%	0.00%	NA
Indica Intermediate	786	99.10%	0.00%	0.89%	0.00%	NA
Temperate Japonica	767	80.60%	18.80%	0.65%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	83.00%	17.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg1219758226	A -> DEL	N	N	silent_mutation	Average:37.353; most accessible tissue: Minghui63 root, score: 82.349	N	N	N	N
vg1219758226	A -> G	LOC_Os12g32710.1	upstream_gene_variant ; 313.0bp to feature; MODIFIER	silent_mutation	Average:37.353; most accessible tissue: Minghui63 root, score: 82.349	N	N	N	N
vg1219758226	A -> G	LOC_Os12g32710-LOC_Os12g32720	intergenic_region ; MODIFIER	silent_mutation	Average:37.353; most accessible tissue: Minghui63 root, score: 82.349	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219758226	1.20E-06	1.20E-06	mr1806	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