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Detailed information for vg0527488306:

Variant ID: vg0527488306 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 27488306
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

TGTACTGGATCGGAGCATTGTTTTTCAATAAACAACAGTTTTCCTTTGCGAGAATCATGCGCATTTAATCTATCATATTGTTTGTAGGCTACTCTCTCTC[C/T]
ATTTTAAAATAAAATGTAAAATATTTAAGGTTTATCTCCACGTTGAACGTTTTCAAGTTTGAATAAATTTATAGAAAAAACCGCAACACAATTTTCAACA

Reverse complement sequence

TGTTGAAAATTGTGTTGCGGTTTTTTCTATAAATTTATTCAAACTTGAAAACGTTCAACGTGGAGATAAACCTTAAATATTTTACATTTTATTTTAAAAT[G/A]
GAGAGAGAGTAGCCTACAAACAATATGATAGATTAAATGCGCATGATTCTCGCAAAGGAAAACTGTTGTTTATTGAAAAACAATGCTCCGATCCAGTACA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.90%	29.10%	0.06%	0.00%	NA
All Indica	2759	96.30%	3.60%	0.07%	0.00%	NA
All Japonica	1512	28.80%	71.20%	0.07%	0.00%	NA
Aus	269	59.10%	40.90%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	86.70%	13.30%	0.00%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	3.90%	0.25%	0.00%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	76.40%	23.60%	0.00%	0.00%	NA
Japonica Intermediate	241	12.90%	86.70%	0.41%	0.00%	NA
VI/Aromatic	96	35.40%	64.60%	0.00%	0.00%	NA
Intermediate	90	72.20%	27.80%	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
vg0527488306	C -> T	LOC_Os05g47950.1	upstream_gene_variant ; 713.0bp to feature; MODIFIER	silent_mutation	Average:46.608; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0527488306	C -> T	LOC_Os05g47940.1	downstream_gene_variant ; 4393.0bp to feature; MODIFIER	silent_mutation	Average:46.608; most accessible tissue: Callus, score: 87.64	N	N	N	N
vg0527488306	C -> T	LOC_Os05g47950-LOC_Os05g47960	intergenic_region ; MODIFIER	silent_mutation	Average:46.608; most accessible tissue: Callus, score: 87.64	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0527488306	NA	4.34E-06	mr1056	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
vg0527488306	NA	4.71E-54	mr1241	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
vg0527488306	NA	3.53E-12	mr1471	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
vg0527488306	NA	6.72E-07	mr1471	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
vg0527488306	NA	2.36E-06	mr1543	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
vg0527488306	NA	1.75E-06	mr1642	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
vg0527488306	NA	4.84E-07	mr1817	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
vg0527488306	NA	1.01E-12	mr1853	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
vg0527488306	NA	1.03E-07	mr1047_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
vg0527488306	NA	1.28E-64	mr1241_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
vg0527488306	NA	2.47E-07	mr1347_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
vg0527488306	NA	1.23E-06	mr1422_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
vg0527488306	NA	5.29E-10	mr1471_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
vg0527488306	NA	4.51E-11	mr1471_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
vg0527488306	NA	1.93E-09	mr1642_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
vg0527488306	NA	8.36E-07	mr1653_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
vg0527488306	NA	5.13E-06	mr1815_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
vg0527488306	NA	1.33E-10	mr1817_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
vg0527488306	NA	2.24E-14	mr1827_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
vg0527488306	NA	8.82E-12	mr1893_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