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Detailed information for vg0611421019:

Variant ID: vg0611421019 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11421019
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTGGAATTTATTAATTAAAATTAGATCTTCTCTTCTAGGCTTTTAAAATAAATTCTAAAAATTCTATTTAAACAACAATTTATATATTTTGAATTTT[C/T]
AGGGTGTGACATATGGTCTACATCAAAGTTGTATAGGTTGGCGCAATCTACAAGATTATGTCTAGATTAACATTTATTATACTCCCTCTGTTTTATAATG

Reverse complement sequence

CATTATAAAACAGAGGGAGTATAATAAATGTTAATCTAGACATAATCTTGTAGATTGCGCCAACCTATACAACTTTGATGTAGACCATATGTCACACCCT[G/A]
AAAATTCAAAATATATAAATTGTTGTTTAAATAGAATTTTTAGAATTTATTTTAAAAGCCTAGAAGAGAAGATCTAATTTTAATTAATAAATTCCAATAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.50%	0.20%	1.59%	2.67%	NA
All Indica	2759	92.90%	0.30%	2.57%	4.17%	NA
All Japonica	1512	99.30%	0.00%	0.20%	0.53%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	98.50%	0.20%	0.43%	0.86%	NA
Indica III	913	88.10%	0.50%	5.48%	5.91%	NA
Indica Intermediate	786	90.20%	0.30%	2.42%	7.12%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.20%	0.00%	0.40%	1.39%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0611421019	C -> T	LOC_Os06g19930.1	upstream_gene_variant ; 4547.0bp to feature; MODIFIER	silent_mutation	Average:25.834; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0611421019	C -> T	LOC_Os06g19950.1	upstream_gene_variant ; 2591.0bp to feature; MODIFIER	silent_mutation	Average:25.834; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0611421019	C -> T	LOC_Os06g19940.1	intron_variant ; MODIFIER	silent_mutation	Average:25.834; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0611421019	C -> DEL	N	N	silent_mutation	Average:25.834; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611421019	7.04E-06	5.69E-06	mr1220_2	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
vg0611421019	NA	2.35E-06	mr1852_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