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Detailed information for vg0911580908:

Variant ID: vg0911580908 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 11580908
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACATGTAAATCATTCACAATTAATTTCTAGTAATTCGTATAGTTTAACAACATATGAACTATTCCCTCCGTCCCAAAATAACTCAACCTAGGATGGGAT[G/A]
TGACCCATCGTAGGCCAACGAATCTGGACATAGGGAATATGTCACATCTAATACTAGGTTGAGTTATTTTGGCATAGAGGGAGTATATATTAAGAAAGTA

Reverse complement sequence

TACTTTCTTAATATATACTCCCTCTATGCCAAAATAACTCAACCTAGTATTAGATGTGACATATTCCCTATGTCCAGATTCGTTGGCCTACGATGGGTCA[C/T]
ATCCCATCCTAGGTTGAGTTATTTTGGGACGGAGGGAATAGTTCATATGTTGTTAAACTATACGAATTACTAGAAATTAATTGTGAATGATTTACATGTT

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	85.90%	1.20%	0.99%	11.93%	NA
All Indica	2759	86.00%	0.40%	1.12%	12.43%	NA
All Japonica	1512	88.40%	2.80%	0.73%	8.13%	NA
Aus	269	67.70%	1.10%	1.49%	29.74%	NA
Indica I	595	98.50%	0.30%	0.17%	1.01%	NA
Indica II	465	76.10%	0.20%	1.94%	21.72%	NA
Indica III	913	84.00%	0.10%	0.77%	15.12%	NA
Indica Intermediate	786	84.70%	1.00%	1.78%	12.47%	NA
Temperate Japonica	767	83.30%	2.20%	1.43%	13.04%	NA
Tropical Japonica	504	93.10%	2.80%	0.00%	4.17%	NA
Japonica Intermediate	241	94.60%	4.60%	0.00%	0.83%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	85.60%	0.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0911580908	G -> DEL	N	N	silent_mutation	Average:30.127; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0911580908	G -> A	LOC_Os09g19350.1	intron_variant ; MODIFIER	silent_mutation	Average:30.127; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0911580908	3.98E-06	8.43E-08	mr1137_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
vg0911580908	NA	4.60E-07	mr1617_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