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Detailed information for vg0611582868:

Variant ID: vg0611582868 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11582868
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTATATGAAGCATAGATGATAGGAATATTTCCCCTACTTACTCAATGGATTAAGTCCTAGCACGTGGGTGTCTCTGGTTAAAACTAATTGGAGAGGCCT[A/C]
TCCAATTAGATTTACCGTTGTAGAAAATCATTTCAAAATCCTCAGAATTTTGGCATGATAAGATATGGTAGAGTATTTGGGATGTGTTTAAATTGCTTCA

Reverse complement sequence

TGAAGCAATTTAAACACATCCCAAATACTCTACCATATCTTATCATGCCAAAATTCTGAGGATTTTGAAATGATTTTCTACAACGGTAAATCTAATTGGA[T/G]
AGGCCTCTCCAATTAGTTTTAACCAGAGACACCCACGTGCTAGGACTTAATCCATTGAGTAAGTAGGGGAAATATTCCTATCATCTATGCTTCATATAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.50%	1.50%	0.04%	0.00%	NA
All Indica	2759	97.80%	2.10%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.80%	4.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	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
vg0611582868	A -> C	LOC_Os06g20200.1	upstream_gene_variant ; 3475.0bp to feature; MODIFIER	silent_mutation	Average:30.866; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0611582868	A -> C	LOC_Os06g20190.1	intron_variant ; MODIFIER	silent_mutation	Average:30.866; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611582868	6.68E-06	9.39E-07	mr1749	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
vg0611582868	NA	2.94E-06	mr1937	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