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Detailed information for vg0921620411:

Variant ID: vg0921620411 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21620411
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTCCTTCAGTTCCCCTCTCAACAATGTGATACTTCCTCCGTTTTTACAATGTAAGTCATTCTATTATTTCCTATATTCATATTTATATTATGAATGTGG[A/G]
AAATTTTAGAATGATTTACATTGTGAAACGGAAGGGAGTATGTTTTTATTCCAGCATGCATGTTGATGGCACTTGGAATCAGCTCTGGTTCAGTTTAAAA

Reverse complement sequence

TTTTAAACTGAACCAGAGCTGATTCCAAGTGCCATCAACATGCATGCTGGAATAAAAACATACTCCCTTCCGTTTCACAATGTAAATCATTCTAAAATTT[T/C]
CCACATTCATAATATAAATATGAATATAGGAAATAATAGAATGACTTACATTGTAAAAACGGAGGAAGTATCACATTGTTGAGAGGGGAACTGAAGGACA

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	94.60%	5.40%	0.02%	0.00%	NA
All Indica	2759	91.40%	8.60%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	91.60%	8.20%	0.22%	0.00%	NA
Indica III	913	86.20%	13.80%	0.00%	0.00%	NA
Indica Intermediate	786	91.20%	8.80%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0921620411	A -> G	LOC_Os09g37510-LOC_Os09g37520	intergenic_region ; MODIFIER	silent_mutation	Average:50.757; most accessible tissue: Callus, score: 73.004	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921620411	NA	9.99E-06	mr1613	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