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Detailed information for vg1226283597:

Variant ID: vg1226283597 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26283597
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGATGACCCTGCCAACTCTCGTAGGGTCGCCTCGCCAAACACATGGAGCTGCTAGAGCTAGCTTATACTCCCGTAGCTTAACTTTTTAAAATATGTTT[G/A]
ACCGTTCGTCTTATTTAAAAAATTTAAGCAATTATTAATTCTTTTTCTACCATTTAATTCATTATTAAATATATTTTTATGTATACATATAGTTTTACTC

Reverse complement sequence

GAGTAAAACTATATGTATACATAAAAATATATTTAATAATGAATTAAATGGTAGAAAAAGAATTAATAATTGCTTAAATTTTTTAAATAAGACGAACGGT[C/T]
AAACATATTTTAAAAAGTTAAGCTACGGGAGTATAAGCTAGCTCTAGCAGCTCCATGTGTTTGGCGAGGCGACCCTACGAGAGTTGGCAGGGTCATCAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.10%	3.40%	7.72%	23.83%	NA
All Indica	2759	53.10%	0.20%	7.47%	39.22%	NA
All Japonica	1512	86.00%	9.30%	4.30%	0.40%	NA
Aus	269	56.10%	2.60%	30.48%	10.78%	NA
Indica I	595	48.10%	0.00%	9.75%	42.18%	NA
Indica II	465	68.80%	0.00%	6.24%	24.95%	NA
Indica III	913	43.90%	0.40%	5.48%	50.16%	NA
Indica Intermediate	786	58.40%	0.10%	8.78%	32.70%	NA
Temperate Japonica	767	79.00%	14.60%	6.26%	0.13%	NA
Tropical Japonica	504	95.80%	1.60%	1.79%	0.79%	NA
Japonica Intermediate	241	88.00%	8.30%	3.32%	0.41%	NA
VI/Aromatic	96	92.70%	2.10%	3.12%	2.08%	NA
Intermediate	90	75.60%	6.70%	10.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1226283597	G -> DEL	N	N	silent_mutation	Average:47.682; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N
vg1226283597	G -> A	LOC_Os12g42280-LOC_Os12g42284	intergenic_region ; MODIFIER	silent_mutation	Average:47.682; most accessible tissue: Zhenshan97 flower, score: 79.53	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226283597	1.09E-06	3.65E-07	mr1521	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