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Detailed information for vg0327579645:

Variant ID: vg0327579645 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27579645
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

TGCATGAATGATGTGGCATATCCACGTGGTATTTTAAGTGAGTCAAGGACTATATTAAGCCGCATGATAATCCTTTAGAACTTATTTGGACATTATAAAA[T/C]
ATTAAGGACTAATTCGATCCCTGAGCAAAAGTTGAAGGAGTGAACTGACTATTCACCCTATAATTTTATAAAAGGAGGGAGTAGTAAGAAAAAGGGCCTT

Reverse complement sequence

AAGGCCCTTTTTCTTACTACTCCCTCCTTTTATAAAATTATAGGGTGAATAGTCAGTTCACTCCTTCAACTTTTGCTCAGGGATCGAATTAGTCCTTAAT[A/G]
TTTTATAATGTCCAAATAAGTTCTAAAGGATTATCATGCGGCTTAATATAGTCCTTGACTCACTTAAAATACCACGTGGATATGCCACATCATTCATGCA

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	74.00%	19.30%	0.85%	5.92%	NA
All Indica	2759	67.80%	20.80%	1.34%	10.00%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	1.90%	97.80%	0.37%	0.00%	NA
Indica I	595	54.30%	1.50%	4.37%	39.83%	NA
Indica II	465	43.90%	54.20%	1.08%	0.86%	NA
Indica III	913	89.20%	10.30%	0.11%	0.44%	NA
Indica Intermediate	786	67.40%	28.00%	0.64%	3.94%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	67.80%	25.60%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0327579645	T -> C	LOC_Os03g48430.1	downstream_gene_variant ; 1264.0bp to feature; MODIFIER	silent_mutation	Average:31.383; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0327579645	T -> C	LOC_Os03g48440.1	downstream_gene_variant ; 4240.0bp to feature; MODIFIER	silent_mutation	Average:31.383; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0327579645	T -> C	LOC_Os03g48410-LOC_Os03g48430	intergenic_region ; MODIFIER	silent_mutation	Average:31.383; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0327579645	T -> DEL	N	N	silent_mutation	Average:31.383; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327579645	1.40E-10	3.73E-20	mr1193	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
vg0327579645	8.75E-09	9.39E-15	mr1193	Ind_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
vg0327579645	NA	2.00E-12	mr1232	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
vg0327579645	NA	1.61E-06	mr1291	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
vg0327579645	NA	5.56E-06	mr1336	Ind_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
vg0327579645	NA	2.29E-10	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
vg0327579645	NA	9.36E-20	mr1557	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
vg0327579645	NA	3.09E-10	mr1722	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
vg0327579645	NA	1.15E-07	mr1815	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
vg0327579645	1.10E-11	4.12E-27	mr1193_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
vg0327579645	5.91E-10	1.86E-12	mr1193_2	Ind_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
vg0327579645	NA	3.27E-10	mr1232_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
vg0327579645	NA	7.64E-06	mr1232_2	Ind_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
vg0327579645	NA	9.31E-18	mr1557_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
vg0327579645	NA	2.06E-08	mr1557_2	Ind_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