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Detailed information for vg0204732555:

Variant ID: vg0204732555 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4732555
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

AAATAGGGAGTTCTCAAGCATCAAGAAACCGGCGTGCCATATTAGCTACAGTTTCTGTATAAAAACGCATGAATACTTTGTTGAGGTAAAACGTAAAAGT[C/T]
GTTTTTAAGTAAGCATGTTTCACAAAATGGTGCACTAAGCACTAGTCTGAGTTTTGAACTGCTATTTGGTGGTGGCTACTTTCTCCTGCTCCGTTAGTAT

Reverse complement sequence

ATACTAACGGAGCAGGAGAAAGTAGCCACCACCAAATAGCAGTTCAAAACTCAGACTAGTGCTTAGTGCACCATTTTGTGAAACATGCTTACTTAAAAAC[G/A]
ACTTTTACGTTTTACCTCAACAAAGTATTCATGCGTTTTTATACAGAAACTGTAGCTAATATGGCACGCCGGTTTCTTGATGCTTGAGAACTCCCTATTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.90%	46.80%	0.23%	0.00%	NA
All Indica	2759	55.90%	43.70%	0.40%	0.00%	NA
All Japonica	1512	59.90%	40.10%	0.00%	0.00%	NA
Aus	269	2.60%	97.40%	0.00%	0.00%	NA
Indica I	595	46.60%	53.40%	0.00%	0.00%	NA
Indica II	465	44.30%	55.70%	0.00%	0.00%	NA
Indica III	913	66.80%	32.10%	1.10%	0.00%	NA
Indica Intermediate	786	57.30%	42.60%	0.13%	0.00%	NA
Temperate Japonica	767	93.90%	6.10%	0.00%	0.00%	NA
Tropical Japonica	504	17.10%	82.90%	0.00%	0.00%	NA
Japonica Intermediate	241	41.10%	58.90%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	46.70%	53.30%	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
vg0204732555	C -> T	LOC_Os02g09210.1	downstream_gene_variant ; 2235.0bp to feature; MODIFIER	silent_mutation	Average:53.421; most accessible tissue: Callus, score: 83.567	N	N	N	N
vg0204732555	C -> T	LOC_Os02g09210-LOC_Os02g09220	intergenic_region ; MODIFIER	silent_mutation	Average:53.421; most accessible tissue: Callus, score: 83.567	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204732555	NA	3.54E-07	mr1271	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
vg0204732555	NA	1.39E-09	mr1295	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
vg0204732555	NA	6.90E-06	mr1808	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
vg0204732555	NA	6.81E-07	mr1870	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
vg0204732555	NA	3.99E-08	mr1031_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
vg0204732555	NA	1.13E-07	mr1125_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
vg0204732555	NA	6.58E-14	mr1241_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
vg0204732555	NA	3.08E-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
vg0204732555	NA	8.90E-06	mr1295_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
vg0204732555	NA	4.22E-06	mr1404_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
vg0204732555	NA	5.61E-08	mr1526_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
vg0204732555	NA	6.41E-09	mr1584_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
vg0204732555	NA	7.58E-07	mr1798_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
vg0204732555	NA	4.42E-09	mr1808_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
vg0204732555	NA	7.00E-08	mr1808_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