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Detailed information for vg0103290887:

Variant ID: vg0103290887 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3290887
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTAATAAAATCATAAAAAATTTAAAAAATTATCACACCAGCAACAACAATTAAAACAGAAACACAAAAGAACCACGTATCCACCGTCCAATTATAATTCC[T/A]
TGCCTCCCGAATTGATGAAACGCGCAAGCGTGCAAGTGTAAGTGTCACAAATGCAGACACATTTATAGGGTGCCTAGTGCTTAGGAGGGCAGATTGCCGG

Reverse complement sequence

CCGGCAATCTGCCCTCCTAAGCACTAGGCACCCTATAAATGTGTCTGCATTTGTGACACTTACACTTGCACGCTTGCGCGTTTCATCAATTCGGGAGGCA[A/T]
GGAATTATAATTGGACGGTGGATACGTGGTTCTTTTGTGTTTCTGTTTTAATTGTTGTTGCTGGTGTGATAATTTTTTAAATTTTTTATGATTTTATTAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	24.50%	10.69%	19.64%	NA
All Indica	2759	50.30%	4.20%	15.59%	29.87%	NA
All Japonica	1512	23.90%	66.80%	3.97%	5.36%	NA
Aus	269	92.90%	3.30%	0.00%	3.72%	NA
Indica I	595	51.40%	1.50%	17.48%	29.58%	NA
Indica II	465	51.60%	2.80%	13.55%	32.04%	NA
Indica III	913	48.10%	7.60%	16.21%	28.15%	NA
Indica Intermediate	786	51.30%	3.30%	14.63%	30.79%	NA
Temperate Japonica	767	29.50%	59.80%	4.56%	6.13%	NA
Tropical Japonica	504	13.30%	78.00%	3.37%	5.36%	NA
Japonica Intermediate	241	28.20%	65.60%	3.32%	2.90%	NA
VI/Aromatic	96	94.80%	4.20%	0.00%	1.04%	NA
Intermediate	90	51.10%	18.90%	16.67%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0103290887	T -> A	LOC_Os01g06940.1	upstream_gene_variant ; 1997.0bp to feature; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> A	LOC_Os01g06920.1	downstream_gene_variant ; 4530.0bp to feature; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> A	LOC_Os01g06950.1	downstream_gene_variant ; 690.0bp to feature; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> A	LOC_Os01g06970.1	downstream_gene_variant ; 2098.0bp to feature; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> A	LOC_Os01g06980.1	downstream_gene_variant ; 3737.0bp to feature; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> A	LOC_Os01g06960.1	intron_variant ; MODIFIER	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0103290887	T -> DEL	N	N	silent_mutation	Average:37.033; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103290887	4.54E-06	4.54E-06	mr1337	Jap_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
vg0103290887	NA	1.51E-08	mr1514	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
vg0103290887	1.50E-06	1.49E-06	mr1954	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
vg0103290887	NA	4.01E-08	mr1821_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