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Detailed information for vg0515924941:

Variant ID: vg0515924941 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15924941
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGGTGCGCGCCGCATAGCCCCTGGTGTATCTCCTTTGCCATTTCTTCGCCTTCGGCAAATGAGATACAACGAAGTAAGGGTTGAAGTACCCCAGTGCG[G/T]
TAAAGCTAACCCGAAACCATCTTATATTTCGTGGCTCTGAGCTGCAAACGCTTCGCTTCTGTTTCGTCTACCGGAAGCCAGCCTGTTTCAAGGTGTTTCA

Reverse complement sequence

TGAAACACCTTGAAACAGGCTGGCTTCCGGTAGACGAAACAGAAGCGAAGCGTTTGCAGCTCAGAGCCACGAAATATAAGATGGTTTCGGGTTAGCTTTA[C/A]
CGCACTGGGGTACTTCAACCCTTACTTCGTTGTATCTCATTTGCCGAAGGCGAAGAAATGGCAAAGGAGATACACCAGGGGCTATGCGGCGCGCACCAGG

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	37.50%	7.60%	22.75%	32.10%	NA
All Indica	2759	17.40%	10.30%	31.53%	40.78%	NA
All Japonica	1512	76.00%	1.10%	1.32%	21.56%	NA
Aus	269	1.50%	20.10%	61.34%	17.10%	NA
Indica I	595	9.60%	4.40%	23.53%	62.52%	NA
Indica II	465	28.40%	4.10%	40.86%	26.67%	NA
Indica III	913	22.10%	16.10%	24.86%	36.91%	NA
Indica Intermediate	786	11.20%	11.80%	39.82%	37.15%	NA
Temperate Japonica	767	93.40%	0.00%	0.39%	6.26%	NA
Tropical Japonica	504	47.40%	3.00%	2.58%	47.02%	NA
Japonica Intermediate	241	80.50%	0.80%	1.66%	17.01%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	52.20%	4.40%	21.11%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515924941	G -> T	LOC_Os05g27380.1	upstream_gene_variant ; 4499.0bp to feature; MODIFIER	silent_mutation	Average:15.925; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg0515924941	G -> T	LOC_Os05g27390.1	downstream_gene_variant ; 2396.0bp to feature; MODIFIER	silent_mutation	Average:15.925; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg0515924941	G -> T	LOC_Os05g27400.1	intron_variant ; MODIFIER	silent_mutation	Average:15.925; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N
vg0515924941	G -> DEL	N	N	silent_mutation	Average:15.925; most accessible tissue: Zhenshan97 root, score: 27.411	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515924941	NA	5.66E-13	Grain_thickness	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
vg0515924941	NA	2.80E-17	Grain_width	Jap_All	YES	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
vg0515924941	NA	8.17E-14	mr1301	Jap_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
vg0515924941	NA	1.30E-13	mr1410	Jap_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
vg0515924941	NA	1.73E-14	mr1771	Jap_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
vg0515924941	NA	6.17E-12	mr1784	Jap_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
vg0515924941	NA	9.34E-08	mr1862	Jap_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
vg0515924941	NA	1.18E-07	mr1993	Jap_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
vg0515924941	NA	1.16E-15	mr1301_2	Jap_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
vg0515924941	NA	7.58E-14	mr1410_2	Jap_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
vg0515924941	NA	4.76E-17	mr1539_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