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Detailed information for vg0611645542:

Variant ID: vg0611645542 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11645542
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

GCACTATATTTTTTTGTCACTTTGTATATTGCCCGATCCGCCACCTTGATACGTTTCCTGCTTCAATTGATTAAAAAATCGATTCCCTACCCCTTTTGAT[T/C]
TGGCTTTAATTTTCCCGGATTTAATCTCCAGCCGCCGCCTAGGCCGACCCCTAACGCCGCCGCCACATCGATCTACCTCCCCGTGCGTTTTCTCTTTTCG

Reverse complement sequence

CGAAAAGAGAAAACGCACGGGGAGGTAGATCGATGTGGCGGCGGCGTTAGGGGTCGGCCTAGGCGGCGGCTGGAGATTAAATCCGGGAAAATTAAAGCCA[A/G]
ATCAAAAGGGGTAGGGAATCGATTTTTTAATCAATTGAAGCAGGAAACGTATCAAGGTGGCGGATCGGGCAATATACAAAGTGACAAAAAAATATAGTGC

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	95.40%	4.00%	0.57%	0.00%	NA
All Indica	2759	92.80%	6.30%	0.98%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	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	92.70%	6.50%	0.86%	0.00%	NA
Indica III	913	88.30%	9.60%	2.08%	0.00%	NA
Indica Intermediate	786	92.50%	7.00%	0.51%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	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
vg0611645542	T -> C	LOC_Os06g20280.1	upstream_gene_variant ; 2228.0bp to feature; MODIFIER	silent_mutation	Average:32.658; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0611645542	T -> C	LOC_Os06g20280-LOC_Os06g20290	intergenic_region ; MODIFIER	silent_mutation	Average:32.658; 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
vg0611645542	2.02E-06	NA	mr1068	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
vg0611645542	7.90E-08	4.30E-09	mr1090	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
vg0611645542	3.09E-06	1.40E-06	mr1094	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
vg0611645542	1.89E-06	NA	mr1111	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
vg0611645542	1.61E-07	6.07E-08	mr1121	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
vg0611645542	1.55E-06	NA	mr1144	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
vg0611645542	2.22E-08	3.24E-09	mr1211	Ind_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
vg0611645542	4.41E-07	NA	mr1068_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
vg0611645542	5.74E-09	5.19E-10	mr1090_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
vg0611645542	NA	2.49E-06	mr1094_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
vg0611645542	4.93E-06	NA	mr1111_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
vg0611645542	9.82E-07	8.75E-08	mr1121_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
vg0611645542	1.05E-08	2.90E-10	mr1211_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