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Detailed information for vg0624640066:

Variant ID: vg0624640066 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24640066
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TAATTAGCATATATTTACTATAGCATCACATAGGCTAATCATGAATTAATCAGGCTCAATATATAGATTTGTCTCATGAATTAGTCCAGAATTATGAAAT[G/A]
TGTTTTATCATTAGTCTATATTTAATACTTCTAATTAGTGTCAAATATCCGATATGACAGGGACTTAAAAAAAATTTAGCCCCATCCACAAACAGCCCCT

Reverse complement sequence

AGGGGCTGTTTGTGGATGGGGCTAAATTTTTTTTAAGTCCCTGTCATATCGGATATTTGACACTAATTAGAAGTATTAAATATAGACTAATGATAAAACA[C/T]
ATTTCATAATTCTGGACTAATTCATGAGACAAATCTATATATTGAGCCTGATTAATTCATGATTAGCCTATGTGATGCTATAGTAAATATATGCTAATTA

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	41.70%	4.40%	0.72%	53.17%	NA
All Indica	2759	9.10%	1.60%	1.16%	88.18%	NA
All Japonica	1512	89.10%	10.20%	0.00%	0.73%	NA
Aus	269	86.20%	0.00%	0.00%	13.75%	NA
Indica I	595	1.70%	0.20%	0.50%	97.65%	NA
Indica II	465	6.20%	3.00%	1.51%	89.25%	NA
Indica III	913	13.40%	0.10%	1.10%	85.43%	NA
Indica Intermediate	786	11.30%	3.60%	1.53%	83.59%	NA
Temperate Japonica	767	98.80%	0.30%	0.00%	0.91%	NA
Tropical Japonica	504	71.00%	28.40%	0.00%	0.60%	NA
Japonica Intermediate	241	95.90%	3.70%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	51.10%	11.10%	2.22%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0624640066	G -> A	LOC_Os06g41170.1	upstream_gene_variant ; 3958.0bp to feature; MODIFIER	silent_mutation	Average:16.506; most accessible tissue: Callus, score: 70.211	N	N	N	N
vg0624640066	G -> A	LOC_Os06g41180.1	downstream_gene_variant ; 2249.0bp to feature; MODIFIER	silent_mutation	Average:16.506; most accessible tissue: Callus, score: 70.211	N	N	N	N
vg0624640066	G -> A	LOC_Os06g41180-LOC_Os06g41190	intergenic_region ; MODIFIER	silent_mutation	Average:16.506; most accessible tissue: Callus, score: 70.211	N	N	N	N
vg0624640066	G -> DEL	N	N	silent_mutation	Average:16.506; most accessible tissue: Callus, score: 70.211	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624640066	NA	7.14E-09	mr1583	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0624640066	4.99E-09	NA	mr1850_2	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
vg0624640066	NA	7.01E-08	mr1850_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251