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Detailed information for vg0619937082:

Variant ID: vg0619937082 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19937082
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TCAGCCCAGCATCAAGAAGCGAACTGCTACTATACCTGGCAGCTTCGCTAGTGGCAGTCAGTGCTGCTCTTGTCCAAGAAACGGATTCAGGCCAAAAACC[G/A]
GTCTATTTCATCTCCGAAGCATTGCAAGGAGCGAAGACAAGATACATTGAAATGGAAAAGCTCGCTTACGCCCTGGTGATGGCTTCACGCAAGATTAAGC

Reverse complement sequence

GCTTAATCTTGCGTGAAGCCATCACCAGGGCGTAAGCGAGCTTTTCCATTTCAATGTATCTTGTCTTCGCTCCTTGCAATGCTTCGGAGATGAAATAGAC[C/T]
GGTTTTTGGCCTGAATCCGTTTCTTGGACAAGAGCAGCACTGACTGCCACTAGCGAAGCTGCCAGGTATAGTAGCAGTTCGCTTCTTGATGCTGGGCTGA

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	48.10%	35.00%	6.09%	10.81%	NA
All Indica	2759	66.80%	5.80%	9.13%	18.34%	NA
All Japonica	1512	6.80%	92.90%	0.13%	0.13%	NA
Aus	269	84.40%	4.10%	11.52%	0.00%	NA
Indica I	595	75.10%	5.50%	8.74%	10.59%	NA
Indica II	465	64.70%	8.20%	10.97%	16.13%	NA
Indica III	913	60.90%	1.40%	8.65%	29.03%	NA
Indica Intermediate	786	68.40%	9.50%	8.91%	13.10%	NA
Temperate Japonica	767	8.50%	91.30%	0.00%	0.26%	NA
Tropical Japonica	504	6.70%	92.90%	0.40%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	39.60%	1.04%	0.00%	NA
Intermediate	90	46.70%	47.80%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0619937082	G -> A	LOC_Os06g34250.1	downstream_gene_variant ; 2005.0bp to feature; MODIFIER	silent_mutation	Average:28.537; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0619937082	G -> A	LOC_Os06g34240.1	intron_variant ; MODIFIER	silent_mutation	Average:28.537; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N
vg0619937082	G -> DEL	N	N	silent_mutation	Average:28.537; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619937082	3.11E-06	3.11E-06	mr1165	Jap_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
vg0619937082	NA	6.89E-06	mr1189	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
vg0619937082	NA	3.86E-06	mr1269	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
vg0619937082	NA	5.40E-07	mr1527	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
vg0619937082	NA	8.03E-08	mr1796	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
vg0619937082	5.58E-06	NA	mr1165_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
vg0619937082	NA	3.29E-07	mr1819_2	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