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Detailed information for vg0501545838:

Variant ID: vg0501545838 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1545838
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTCCTTTTACCACTAATTCAACTGATTAGGTACAATAGATTCATATTTTAGGATAACTTATTATATATTTTTTCGATAACAAGTTTTTTTCGATAAC[A/G]
AGGAAGAGGCGAAGAGCACATATGAGCACACCAGTATCTATTGTCCTACGCACACTATAATCAAACACTTGCGAATGCGCCTCATAAAACATGCTAAGAT

Reverse complement sequence

ATCTTAGCATGTTTTATGAGGCGCATTCGCAAGTGTTTGATTATAGTGTGCGTAGGACAATAGATACTGGTGTGCTCATATGTGCTCTTCGCCTCTTCCT[T/C]
GTTATCGAAAAAAACTTGTTATCGAAAAAATATATAATAAGTTATCCTAAAATATGAATCTATTGTACCTAATCAGTTGAATTAGTGGTAAAAGGAAAAG

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	96.60%	2.70%	0.74%	0.00%	NA
All Indica	2759	94.20%	4.60%	1.23%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	78.70%	16.60%	4.73%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	92.50%	6.20%	1.27%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg0501545838	A -> G	LOC_Os05g03620.1	upstream_gene_variant ; 1595.0bp to feature; MODIFIER	silent_mutation	Average:61.71; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0501545838	A -> G	LOC_Os05g03610.1	downstream_gene_variant ; 4267.0bp to feature; MODIFIER	silent_mutation	Average:61.71; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0501545838	A -> G	LOC_Os05g03610-LOC_Os05g03620	intergenic_region ; MODIFIER	silent_mutation	Average:61.71; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501545838	NA	4.56E-06	Grain_weight	Ind_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