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Detailed information for vg0232481675:

Variant ID: vg0232481675 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32481675
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTGAGCATTTTTGCTCATATTTTTCTCTTTTTATTCCGGGTACGTCCCTGTCATCAAGACTGTTTCTAGGGATTCGGCACCCATTATTTTGCTCACATC[G/A]
AATACGTCCTTGTCGTCAAGACTGTTTCCAAGGATTCGGTATTTATTTTTTTCTCATATTTTTATTCTGTTTTTCACAATGAGCAATTAAAGCTATTTGA

Reverse complement sequence

TCAAATAGCTTTAATTGCTCATTGTGAAAAACAGAATAAAAATATGAGAAAAAAATAAATACCGAATCCTTGGAAACAGTCTTGACGACAAGGACGTATT[C/T]
GATGTGAGCAAAATAATGGGTGCCGAATCCCTAGAAACAGTCTTGATGACAGGGACGTACCCGGAATAAAAAGAGAAAAATATGAGCAAAAATGCTCAAG

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	97.10%	2.80%	0.06%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	91.30%	8.50%	0.13%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	86.80%	13.20%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.40%	0.20%	0.00%	NA
Japonica Intermediate	241	92.90%	6.60%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0232481675	G -> A	LOC_Os02g53090.1	downstream_gene_variant ; 1720.0bp to feature; MODIFIER	silent_mutation	Average:14.757; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0232481675	G -> A	LOC_Os02g53080-LOC_Os02g53090	intergenic_region ; MODIFIER	silent_mutation	Average:14.757; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232481675	NA	3.08E-06	mr1296_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
vg0232481675	3.98E-06	3.98E-06	mr1371_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
vg0232481675	6.03E-06	6.03E-06	mr1494_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
vg0232481675	NA	9.22E-06	mr1499_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
vg0232481675	4.22E-07	4.22E-07	mr1499_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
vg0232481675	2.11E-06	2.11E-06	mr1616_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
vg0232481675	6.33E-06	6.33E-06	mr1876_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
vg0232481675	NA	3.40E-06	mr1910_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
vg0232481675	1.35E-09	1.67E-11	mr1946_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
vg0232481675	NA	1.45E-07	mr1946_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
vg0232481675	1.35E-09	1.67E-11	mr1948_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
vg0232481675	NA	1.45E-07	mr1948_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
vg0232481675	5.38E-06	9.85E-08	mr1977_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
vg0232481675	3.73E-06	8.35E-08	mr1977_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