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Detailed information for vg1021348723:

Variant ID: vg1021348723 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 21348723
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTAATCCATGATTAGCCTATGTGATGCTACAGTAAAAATTCTCTAATTATAGATTAATTAGGCTTAAAAAATTTGTCTCGTGAATTAGCTTTCATTTAT[G/A]
TAATTAGTTTTGTAAGTAATCTATATTTAATACTCTAAAATAGCGTATAAATACAGGGACTAGAGTTAAGTCTCTGAATCTAAACACCACCTTATTTGAT

Reverse complement sequence

ATCAAATAAGGTGGTGTTTAGATTCAGAGACTTAACTCTAGTCCCTGTATTTATACGCTATTTTAGAGTATTAAATATAGATTACTTACAAAACTAATTA[C/T]
ATAAATGAAAGCTAATTCACGAGACAAATTTTTTAAGCCTAATTAATCTATAATTAGAGAATTTTTACTGTAGCATCACATAGGCTAATCATGGATTAAT

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	70.80%	28.30%	0.89%	0.00%	NA
All Indica	2759	99.30%	0.60%	0.14%	0.00%	NA
All Japonica	1512	18.10%	79.50%	2.45%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.70%	1.30%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	0.80%	0.51%	0.00%	NA
Temperate Japonica	767	32.30%	63.00%	4.69%	0.00%	NA
Tropical Japonica	504	3.40%	96.40%	0.20%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	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
vg1021348723	G -> A	LOC_Os10g39910.1	upstream_gene_variant ; 1189.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021348723	G -> A	LOC_Os10g39900.1	downstream_gene_variant ; 643.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1021348723	G -> A	LOC_Os10g39900-LOC_Os10g39910	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1021348723	2.68E-07	1.28E-25	Yield	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
vg1021348723	NA	1.96E-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
vg1021348723	NA	2.77E-09	mr1322	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