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Detailed information for vg0719508934:

Variant ID: vg0719508934 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19508934
Reference Allele: C	Alternative Allele: A,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAAAAATTTTGTCTCATAAATTAAGGGCAAACTAAAGTTCGGATAATATTATTTTATAATAATTTAAGGGTTCTATTTTTCTTAAGGTATCTTAAAAAA[C/A,T]
CATTCACAAAATTTTTCTTAAGGTATGACTTTTGAATCATTTTTTTCTCGAGTAAATAAGAAACCATTGCTAGTTAATTATCATACAGTCCATTTATATA

Reverse complement sequence

TATATAAATGGACTGTATGATAATTAACTAGCAATGGTTTCTTATTTACTCGAGAAAAAAATGATTCAAAAGTCATACCTTAAGAAAAATTTTGTGAATG[G/T,A]
TTTTTTAAGATACCTTAAGAAAAATAGAACCCTTAAATTATTATAAAATAATATTATCCGAACTTTAGTTTGCCCTTAATTTATGAGACAAAATTTTTGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	9.20%	0.00%	0.00%	T: 0.02%
All Indica	2759	86.80%	13.10%	0.00%	0.00%	T: 0.04%
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	75.50%	24.50%	0.00%	0.00%	NA
Indica I	595	92.90%	7.10%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	78.00%	22.00%	0.00%	0.00%	NA
Indica Intermediate	786	85.10%	14.80%	0.00%	0.00%	T: 0.13%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0719508934	C -> A	LOC_Os07g32670.1	downstream_gene_variant ; 3775.0bp to feature; MODIFIER	silent_mutation	Average:35.806; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0719508934	C -> A	LOC_Os07g32670-LOC_Os07g32680	intergenic_region ; MODIFIER	silent_mutation	Average:35.806; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0719508934	C -> T	LOC_Os07g32670.1	downstream_gene_variant ; 3775.0bp to feature; MODIFIER	silent_mutation	Average:35.806; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0719508934	C -> T	LOC_Os07g32670-LOC_Os07g32680	intergenic_region ; MODIFIER	silent_mutation	Average:35.806; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719508934	4.45E-06	NA	mr1151_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
vg0719508934	5.70E-06	NA	mr1248_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
vg0719508934	7.86E-06	NA	mr1423_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
vg0719508934	8.39E-06	8.39E-06	mr1447_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
vg0719508934	8.00E-06	NA	mr1595_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
vg0719508934	NA	3.22E-06	mr1785_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
vg0719508934	6.96E-06	NA	mr1795_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
vg0719508934	6.90E-06	NA	mr1800_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
vg0719508934	1.06E-06	1.05E-06	mr1953_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