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Detailed information for vg0624711737:

Variant ID: vg0624711737 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24711737
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTCACTAAGTTACTTCTTAGACATATAAAAGTAAATTTAGTAAAGGTTAAAAGTAATTTACATATATATTACAGAAGTAACTTATAATAAAAAGGAAA[G/A]
TAACTTTAATTTAGAACTATATCTAGATTCATTAACATCTATATAAATATGGGCAATGCTAAAATAACTTATATTATGAAACGGGGGAGTAACTCTCTTT

Reverse complement sequence

AAAGAGAGTTACTCCCCCGTTTCATAATATAAGTTATTTTAGCATTGCCCATATTTATATAGATGTTAATGAATCTAGATATAGTTCTAAATTAAAGTTA[C/T]
TTTCCTTTTTATTATAAGTTACTTCTGTAATATATATGTAAATTACTTTTAACCTTTACTAAATTTACTTTTATATGTCTAAGAAGTAACTTAGTGAAAT

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	49.60%	0.10%	7.17%	43.08%	NA
All Indica	2759	23.30%	0.10%	10.22%	66.36%	NA
All Japonica	1512	99.30%	0.00%	0.07%	0.60%	NA
Aus	269	23.80%	0.40%	17.10%	58.74%	NA
Indica I	595	14.60%	0.00%	10.76%	74.62%	NA
Indica II	465	18.10%	0.00%	8.17%	73.76%	NA
Indica III	913	31.10%	0.40%	10.73%	57.72%	NA
Indica Intermediate	786	23.80%	0.00%	10.43%	65.78%	NA
Temperate Japonica	767	98.80%	0.00%	0.13%	1.04%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	0.00%	3.12%	11.46%	NA
Intermediate	90	62.20%	0.00%	7.78%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624711737	G -> A	LOC_Os06g41300.1	upstream_gene_variant ; 772.0bp to feature; MODIFIER	silent_mutation	Average:10.228; most accessible tissue: Callus, score: 30.323	N	N	N	N
vg0624711737	G -> A	LOC_Os06g41310.1	upstream_gene_variant ; 4121.0bp to feature; MODIFIER	silent_mutation	Average:10.228; most accessible tissue: Callus, score: 30.323	N	N	N	N
vg0624711737	G -> A	LOC_Os06g41290.1	downstream_gene_variant ; 4196.0bp to feature; MODIFIER	silent_mutation	Average:10.228; most accessible tissue: Callus, score: 30.323	N	N	N	N
vg0624711737	G -> A	LOC_Os06g41290-LOC_Os06g41300	intergenic_region ; MODIFIER	silent_mutation	Average:10.228; most accessible tissue: Callus, score: 30.323	N	N	N	N
vg0624711737	G -> DEL	N	N	silent_mutation	Average:10.228; most accessible tissue: Callus, score: 30.323	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624711737	6.17E-07	4.63E-06	mr1645_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