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Detailed information for vg0906482532:

Variant ID: vg0906482532 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6482532
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATGCAAAGAGTGCTCAATCACCTCTCTAGGAATACCAGGCATATCGGATGGTTTCCACGCGAAGATATTTTTATTATTTTGAAGAAAGGTGACGAGC[G/A]
CGCTTTCCTATTTACAATCTAACTCGGCGCCTACTACAGCAGTTTTAGTAGGATCAGAAGGATCTAGGGGGATTTTCTTGGTCTTGGCTTCGCTTCCTCC

Reverse complement sequence

GGAGGAAGCGAAGCCAAGACCAAGAAAATCCCCCTAGATCCTTCTGATCCTACTAAAACTGCTGTAGTAGGCGCCGAGTTAGATTGTAAATAGGAAAGCG[C/T]
GCTCGTCACCTTTCTTCAAAATAATAAAAATATCTTCGCGTGGAAACCATCCGATATGCCTGGTATTCCTAGAGAGGTGATTGAGCACTCTTTGCATGTT

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	64.70%	0.60%	3.58%	31.13%	NA
All Indica	2759	45.30%	0.90%	5.65%	48.13%	NA
All Japonica	1512	99.70%	0.00%	0.00%	0.33%	NA
Aus	269	57.60%	0.40%	3.72%	38.29%	NA
Indica I	595	40.20%	0.20%	2.52%	57.14%	NA
Indica II	465	36.60%	1.10%	4.73%	57.63%	NA
Indica III	913	49.40%	1.80%	8.32%	40.53%	NA
Indica Intermediate	786	49.50%	0.50%	5.47%	44.53%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.60%	0.00%	0.00%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	81.20%	0.00%	2.08%	16.67%	NA
Intermediate	90	77.80%	0.00%	1.11%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906482532	G -> DEL	N	N	silent_mutation	Average:32.303; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0906482532	G -> A	LOC_Os09g11600.1	downstream_gene_variant ; 3540.0bp to feature; MODIFIER	silent_mutation	Average:32.303; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0906482532	G -> A	LOC_Os09g11610.1	intron_variant ; MODIFIER	silent_mutation	Average:32.303; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906482532	2.60E-06	NA	mr1721_2	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