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Detailed information for vg0611109671:

Variant ID: vg0611109671 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11109671
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ACTACTGTAAGATTGTTAGAAATTCTTTGTATTGCTTGTGACTGTAATCGAGAGGGTCCAAGACTACCACGATTCCGTCTTTAGGGTGGATGAGTAAACA[G/T]
ATATAATGATCGCTACATATTAACAACAGTATAGTTAGTTAGTACCAGCTAAAATAAGACATATGTGTACAAGATAAATGTACCAGACTTACTTAAAATT

Reverse complement sequence

AATTTTAAGTAAGTCTGGTACATTTATCTTGTACACATATGTCTTATTTTAGCTGGTACTAACTAACTATACTGTTGTTAATATGTAGCGATCATTATAT[C/A]
TGTTTACTCATCCACCCTAAAGACGGAATCGTGGTAGTCTTGGACCCTCTCGATTACAGTCACAAGCAATACAAAGAATTTCTAACAATCTTACAGTAGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.90%	8.40%	9.20%	1.50%	NA
All Indica	2759	68.90%	13.20%	15.33%	2.57%	NA
All Japonica	1512	98.30%	1.30%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	33.80%	23.90%	36.30%	6.05%	NA
Indica II	465	93.50%	3.20%	3.01%	0.22%	NA
Indica III	913	79.40%	12.20%	6.68%	1.75%	NA
Indica Intermediate	786	68.60%	12.30%	16.79%	2.29%	NA
Temperate Japonica	767	98.20%	1.60%	0.26%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	96.70%	2.50%	0.83%	0.00%	NA
VI/Aromatic	96	92.70%	4.20%	3.12%	0.00%	NA
Intermediate	90	88.90%	7.80%	3.33%	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
vg0611109671	G -> T	LOC_Os06g19500.1	upstream_gene_variant ; 4482.0bp to feature; MODIFIER	silent_mutation	Average:22.981; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0611109671	G -> T	LOC_Os06g19520.1	downstream_gene_variant ; 2348.0bp to feature; MODIFIER	silent_mutation	Average:22.981; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0611109671	G -> T	LOC_Os06g19510.1	intron_variant ; MODIFIER	silent_mutation	Average:22.981; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0611109671	G -> DEL	N	N	silent_mutation	Average:22.981; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611109671	NA	8.08E-06	mr1074	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
vg0611109671	1.48E-06	NA	mr1255_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
vg0611109671	2.28E-06	NA	mr1255_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