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Detailed information for vg0212235071:

Variant ID: vg0212235071 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 12235071
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGAGTGGAGTGCAACCACAATAATCCATGACTGGTGGGCAGAGCTAGCAACCACCAAATGACTATTGAAAAAGGGAGTCTACACCTAATCCTCCTCACG[G/A]
CATGGGAAGTCTGGAAGGAAAGAAACAAAAGAGTCTTCCAGCATAAGGAGTTTATATCCATCAGATCCTTGGGAGCAAAGATCAAGGAGGAAGGCAAAAC

Reverse complement sequence

GTTTTGCCTTCCTCCTTGATCTTTGCTCCCAAGGATCTGATGGATATAAACTCCTTATGCTGGAAGACTCTTTTGTTTCTTTCCTTCCAGACTTCCCATG[C/T]
CGTGAGGAGGATTAGGTGTAGACTCCCTTTTTCAATAGTCATTTGGTGGTTGCTAGCTCTGCCCACCAGTCATGGATTATTGTGGTTGCACTCCACTCTG

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	96.10%	3.40%	0.53%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	88.00%	10.40%	1.59%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	76.90%	19.90%	3.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0212235071	G -> A	LOC_Os02g20720-LOC_Os02g20729	intergenic_region ; MODIFIER	silent_mutation	Average:52.7; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0212235071	1.68E-08	NA	Awn_length	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
vg0212235071	2.28E-07	2.43E-11	mr1693_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0212235071	NA	4.30E-08	mr1693_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