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Detailed information for vg0202024716:

Variant ID: vg0202024716 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2024716
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGTTTAGTTCACGCCAAAATTTAAAGTTTGGTTGAAATTGGAACGATGTGGCGGAAAAGTTAGAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATG[G/A]
AAAAGTTAGAAGTTTGGAACTAAACTCGGCCTAAACCTTTTTTTTTTACTCGGGAACGGTTTGATGAAATCCTGGCTGTATTGCTGTTTTAGAAAACTCT

Reverse complement sequence

AGAGTTTTCTAAAACAGCAATACAGCCAGGATTTCATCAAACCGTTCCCGAGTAAAAAAAAAAGGTTTAGGCCGAGTTTAGTTCCAAACTTCTAACTTTT[C/T]
CATCACATCAAAACTTTCCTACACACACAAACTTCTAACTTTTCCGCCACATCGTTCCAATTTCAACCAAACTTTAAATTTTGGCGTGAACTAAACACAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.60%	8.40%	0.06%	0.00%	NA
All Indica	2759	85.70%	14.20%	0.07%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	97.10%	2.70%	0.17%	0.00%	NA
Indica II	465	88.20%	11.80%	0.00%	0.00%	NA
Indica III	913	75.40%	24.60%	0.00%	0.00%	NA
Indica Intermediate	786	87.70%	12.20%	0.13%	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%	2.20%	0.00%	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
vg0202024716	G -> A	LOC_Os02g04540.1	upstream_gene_variant ; 1228.0bp to feature; MODIFIER	silent_mutation	Average:43.075; most accessible tissue: Callus, score: 79.294	N	N	N	N
vg0202024716	G -> A	LOC_Os02g04540-LOC_Os02g04550	intergenic_region ; MODIFIER	silent_mutation	Average:43.075; most accessible tissue: Callus, score: 79.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202024716	NA	2.85E-08	Grain_thickness	Ind_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
vg0202024716	NA	1.21E-09	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