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Detailed information for vg0507099666:

Variant ID: vg0507099666 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7099666
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, A: 0.05, T: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGTTCGCCCCCGCGAGGGCCGAGGAAGCCTTTCCGGCCCAACAAGCCTAGGGGCTATAGGGCCGGCGATCGCCAGACGGCCCATCAGGGGCCCATGAG[C/A]
CCCTATAATATTATGTACCCCTGTAAATGTCCTTTTCGTAAGGGTAATCATGTAAATTCCCCTGTACAACCTAAACCCTAATAGTAAGAACCTGTAATGG

Reverse complement sequence

CCATTACAGGTTCTTACTATTAGGGTTTAGGTTGTACAGGGGAATTTACATGATTACCCTTACGAAAAGGACATTTACAGGGGTACATAATATTATAGGG[G/T]
CTCATGGGCCCCTGATGGGCCGTCTGGCGATCGCCGGCCCTATAGCCCCTAGGCTTGTTGGGCCGGAAAGGCTTCCTCGGCCCTCGCGGGGGCGAACTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.00%	23.20%	0.89%	36.90%	NA
All Indica	2759	55.50%	7.40%	1.12%	35.99%	NA
All Japonica	1512	4.60%	56.90%	0.40%	38.16%	NA
Aus	269	79.90%	1.50%	0.74%	17.84%	NA
Indica I	595	71.10%	12.80%	1.01%	15.13%	NA
Indica II	465	26.20%	3.70%	1.51%	68.60%	NA
Indica III	913	54.50%	6.70%	1.10%	37.68%	NA
Indica Intermediate	786	62.00%	6.50%	1.02%	30.53%	NA
Temperate Japonica	767	0.70%	91.10%	0.00%	8.21%	NA
Tropical Japonica	504	5.80%	9.90%	0.79%	83.53%	NA
Japonica Intermediate	241	14.50%	46.10%	0.83%	38.59%	NA
VI/Aromatic	96	4.20%	3.10%	1.04%	91.67%	NA
Intermediate	90	30.00%	25.60%	2.22%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507099666	C -> DEL	N	N	silent_mutation	Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0507099666	C -> A	LOC_Os05g12350.1	upstream_gene_variant ; 260.0bp to feature; MODIFIER	silent_mutation	Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0507099666	C -> A	LOC_Os05g12350-LOC_Os05g12360	intergenic_region ; MODIFIER	silent_mutation	Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507099666	NA	9.94E-06	mr1094_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
vg0507099666	NA	1.53E-06	mr1109_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
vg0507099666	3.25E-06	3.25E-06	mr1234_2	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
vg0507099666	NA	8.71E-06	mr1246_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
vg0507099666	NA	1.76E-06	mr1257_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
vg0507099666	NA	2.69E-06	mr1786_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
vg0507099666	NA	5.94E-06	mr1892_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