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Detailed information for vg0320911578:

Variant ID: vg0320911578 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20911578
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.87, C: 0.13, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTTAAGTAAAAATACAATGGTACACACAAAAAAAATAATTCCTCCGTTTCATATTATAAGTCGTTTAACTTTTTTTTCTATTCAAACATTTTTAAGTT[T/C]
AATCAAGTTTATAGAAAAATATAGTAGTATTTTTAACCCAAAACAAACATATTATCAAAATATAATTAATATTTCATTTAATAAAACTAATTTGATATTT

Reverse complement sequence

AAATATCAAATTAGTTTTATTAAATGAAATATTAATTATATTTTGATAATATGTTTGTTTTGGGTTAAAAATACTACTATATTTTTCTATAAACTTGATT[A/G]
AACTTAAAAATGTTTGAATAGAAAAAAAAGTTAAACGACTTATAATATGAAACGGAGGAATTATTTTTTTTGTGTGTACCATTGTATTTTTACTTAACAG

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	85.90%	13.80%	0.28%	0.00%	NA
All Indica	2759	80.10%	19.60%	0.36%	0.00%	NA
All Japonica	1512	93.00%	6.90%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	76.60%	23.20%	0.22%	0.00%	NA
Indica III	913	69.40%	30.10%	0.44%	0.00%	NA
Indica Intermediate	786	83.80%	15.50%	0.64%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	80.60%	19.40%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	2.90%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0320911578	T -> C	LOC_Os03g37710.1	upstream_gene_variant ; 543.0bp to feature; MODIFIER	silent_mutation	Average:67.495; most accessible tissue: Minghui63 root, score: 90.598	N	N	N	N
vg0320911578	T -> C	LOC_Os03g37700.1	downstream_gene_variant ; 3050.0bp to feature; MODIFIER	silent_mutation	Average:67.495; most accessible tissue: Minghui63 root, score: 90.598	N	N	N	N
vg0320911578	T -> C	LOC_Os03g37720.1	downstream_gene_variant ; 2032.0bp to feature; MODIFIER	silent_mutation	Average:67.495; most accessible tissue: Minghui63 root, score: 90.598	N	N	N	N
vg0320911578	T -> C	LOC_Os03g37710-LOC_Os03g37720	intergenic_region ; MODIFIER	silent_mutation	Average:67.495; most accessible tissue: Minghui63 root, score: 90.598	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320911578	NA	1.18E-09	mr1217	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
vg0320911578	NA	7.09E-07	mr1227	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
vg0320911578	1.61E-10	7.98E-12	mr1439	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
vg0320911578	2.22E-06	8.73E-08	mr1439	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
vg0320911578	NA	1.87E-08	mr1845	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