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Detailed information for vg0317018800:

Variant ID: vg0317018800 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17018800
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

ACCACTTGCACTAACCTGCGAGATCCCGAAAGGCGAACCCAAAATCCCGGCCTGATCAGAGCAGCTGGCCACCCGCTTCATCGAACGGGCCAACTCAGCA[C/A]
ACTCTTGCTGCACCTTGCCGACGGAATCCATGGCGAGATCCACCTTGGTAGTCACCTTCTCGAGACTGCCACTTTGGGAATCCAGCCGCTGATCAATCTC

Reverse complement sequence

GAGATTGATCAGCGGCTGGATTCCCAAAGTGGCAGTCTCGAGAAGGTGACTACCAAGGTGGATCTCGCCATGGATTCCGTCGGCAAGGTGCAGCAAGAGT[G/T]
TGCTGAGTTGGCCCGTTCGATGAAGCGGGTGGCCAGCTGCTCTGATCAGGCCGGGATTTTGGGTTCGCCTTTCGGGATCTCGCAGGTTAGTGCAAGTGGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.40%	3.40%	0.19%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	88.70%	10.70%	0.60%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	78.50%	20.30%	1.17%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	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
vg0317018800	C -> A	LOC_Os03g29864.1	missense_variant ; p.Cys505Phe; MODERATE	nonsynonymous_codon ; C505F	Average:34.413; most accessible tissue: Minghui63 flag leaf, score: 72.028	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317018800	NA	2.38E-06	mr1210	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
vg0317018800	1.81E-06	7.03E-08	mr1897	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
vg0317018800	NA	6.12E-06	mr1305_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
vg0317018800	NA	4.36E-07	mr1733_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