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Detailed information for vg0523572518:

Variant ID: vg0523572518 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23572518
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGCGCCTTCTTATATAGAGAGGTGGGGTGGGGTGGTTAGGGCAACTCGCCTCTGGGCCACGGGACGCCGAAAAGAGAGAAAATCTTGAGCAGGCCGAA[G/A]
TGTACGCTACCCAAACTGGGCCGGAATACGCGCCATCAACACATCATGGGCCTCTTTATTAACAGAGAGCAATAGGAATAAGTTCACTTTGTGACCCTCA

Reverse complement sequence

TGAGGGTCACAAAGTGAACTTATTCCTATTGCTCTCTGTTAATAAAGAGGCCCATGATGTGTTGATGGCGCGTATTCCGGCCCAGTTTGGGTAGCGTACA[C/T]
TTCGGCCTGCTCAAGATTTTCTCTCTTTTCGGCGTCCCGTGGCCCAGAGGCGAGTTGCCCTAACCACCCCACCCCACCTCTCTATATAAGAAGGCGCTGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	32.10%	15.10%	6.43%	46.36%	NA
All Indica	2759	22.50%	0.50%	9.28%	67.74%	NA
All Japonica	1512	52.60%	45.20%	2.12%	0.07%	NA
Aus	269	2.20%	0.40%	1.49%	95.91%	NA
Indica I	595	8.90%	0.30%	5.88%	84.87%	NA
Indica II	465	34.00%	0.60%	8.17%	57.20%	NA
Indica III	913	23.10%	0.30%	11.17%	65.39%	NA
Indica Intermediate	786	25.20%	0.80%	10.31%	63.74%	NA
Temperate Japonica	767	30.60%	66.60%	2.61%	0.13%	NA
Tropical Japonica	504	86.70%	11.30%	1.98%	0.00%	NA
Japonica Intermediate	241	51.50%	47.70%	0.83%	0.00%	NA
VI/Aromatic	96	65.60%	0.00%	0.00%	34.38%	NA
Intermediate	90	37.80%	15.60%	13.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0523572518	G -> DEL	N	N	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N
vg0523572518	G -> A	LOC_Os05g40110.1	upstream_gene_variant ; 1860.0bp to feature; MODIFIER	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N
vg0523572518	G -> A	LOC_Os05g40120.1	upstream_gene_variant ; 337.0bp to feature; MODIFIER	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N
vg0523572518	G -> A	LOC_Os05g40140.1	upstream_gene_variant ; 2540.0bp to feature; MODIFIER	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N
vg0523572518	G -> A	LOC_Os05g40130.1	downstream_gene_variant ; 164.0bp to feature; MODIFIER	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N
vg0523572518	G -> A	LOC_Os05g40120-LOC_Os05g40130	intergenic_region ; MODIFIER	silent_mutation	Average:53.777; most accessible tissue: Callus, score: 99.158	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523572518	NA	5.70E-35	Grain_thickness	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
vg0523572518	NA	1.02E-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
vg0523572518	4.13E-08	2.34E-10	Grain_weight	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
vg0523572518	NA	3.85E-09	mr1593	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