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Detailed information for vg0101948831:

Variant ID: vg0101948831 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1948831
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

GTATATATAACATCGGAATTCAAAAACGTTTGCATGATGTTTGCAACCTGAAAAGCTCTTTATTTATTCCTCAACGAGCAAGAACTAAGAAGGCGATTAC[A/T]
CAAGTACTCACAAAGGAATACATGAAACCGGCCGACTCAGCCACTCGGACTCCCAACGGGTACGACACACCAGCAGCAGACCATACTTGCACGACCAAAC

Reverse complement sequence

GTTTGGTCGTGCAAGTATGGTCTGCTGCTGGTGTGTCGTACCCGTTGGGAGTCCGAGTGGCTGAGTCGGCCGGTTTCATGTATTCCTTTGTGAGTACTTG[T/A]
GTAATCGCCTTCTTAGTTCTTGCTCGTTGAGGAATAAATAAAGAGCTTTTCAGGTTGCAAACATCATGCAAACGTTTTTGAATTCCGATGTTATATATAC

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	58.90%	40.80%	0.08%	0.23%	NA
All Indica	2759	85.10%	14.40%	0.11%	0.40%	NA
All Japonica	1512	24.10%	75.90%	0.00%	0.00%	NA
Aus	269	7.10%	92.90%	0.00%	0.00%	NA
Indica I	595	97.30%	2.40%	0.17%	0.17%	NA
Indica II	465	94.20%	5.60%	0.00%	0.22%	NA
Indica III	913	76.10%	23.40%	0.11%	0.33%	NA
Indica Intermediate	786	80.80%	18.30%	0.13%	0.76%	NA
Temperate Japonica	767	15.50%	84.50%	0.00%	0.00%	NA
Tropical Japonica	504	45.00%	55.00%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	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
vg0101948831	A -> T	LOC_Os01g04370.1	3_prime_UTR_variant ; 174.0bp to feature; MODIFIER	silent_mutation	Average:67.925; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N
vg0101948831	A -> T	LOC_Os01g04360.1	upstream_gene_variant ; 3796.0bp to feature; MODIFIER	silent_mutation	Average:67.925; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N
vg0101948831	A -> T	LOC_Os01g04380.1	upstream_gene_variant ; 3097.0bp to feature; MODIFIER	silent_mutation	Average:67.925; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N
vg0101948831	A -> DEL	N	N	silent_mutation	Average:67.925; most accessible tissue: Zhenshan97 flower, score: 82.111	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101948831	NA	1.31E-06	Yield	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0101948831	NA	1.19E-08	mr1465	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
vg0101948831	NA	1.82E-06	mr1925	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
vg0101948831	NA	2.48E-10	mr1228_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
vg0101948831	NA	6.90E-22	mr1401_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