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Detailed information for vg0816293722:

Variant ID: vg0816293722 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16293722
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAGCAGGGAACATGAATTATTTAAGCAGAACCAGAATCCAGAATATTAAAACAAGAATAACATCGTACACATAAGATCAACTTGAAATCTAAATGGCG[T/A]
GAACAATAATATGAACATAAGCAGTTAATTATCACGTAGAAATATATCAGAAACAAATAGATAGAGTAAACAATCCATGAATAACTCAATTTGTTCGTCA

Reverse complement sequence

TGACGAACAAATTGAGTTATTCATGGATTGTTTACTCTATCTATTTGTTTCTGATATATTTCTACGTGATAATTAACTGCTTATGTTCATATTATTGTTC[A/T]
CGCCATTTAGATTTCAAGTTGATCTTATGTGTACGATGTTATTCTTGTTTTAATATTCTGGATTCTGGTTCTGCTTAAATAATTCATGTTCCCTGCTTGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.20%	0.20%	6.47%	60.11%	NA
All Indica	2759	9.50%	0.00%	8.23%	82.28%	NA
All Japonica	1512	73.50%	0.70%	2.05%	23.68%	NA
Aus	269	20.10%	0.00%	16.73%	63.20%	NA
Indica I	595	8.20%	0.00%	8.74%	83.03%	NA
Indica II	465	9.90%	0.00%	2.15%	87.96%	NA
Indica III	913	10.00%	0.00%	11.28%	78.75%	NA
Indica Intermediate	786	9.70%	0.00%	7.89%	82.44%	NA
Temperate Japonica	767	97.90%	0.00%	0.00%	2.09%	NA
Tropical Japonica	504	36.30%	2.20%	4.96%	56.55%	NA
Japonica Intermediate	241	73.90%	0.00%	2.49%	23.65%	NA
VI/Aromatic	96	96.90%	0.00%	0.00%	3.12%	NA
Intermediate	90	52.20%	0.00%	3.33%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816293722	T -> A	LOC_Os08g26800-LOC_Os08g26810	intergenic_region ; MODIFIER	silent_mutation	Average:15.702; most accessible tissue: Callus, score: 40.648	N	N	N	N
vg0816293722	T -> DEL	N	N	silent_mutation	Average:15.702; most accessible tissue: Callus, score: 40.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816293722	4.73E-06	NA	mr1016	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
vg0816293722	3.05E-06	NA	mr1017	Jap_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
vg0816293722	1.03E-06	NA	mr1055	Jap_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
vg0816293722	NA	2.41E-06	mr1124	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
vg0816293722	NA	6.39E-07	mr1136	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
vg0816293722	8.94E-06	NA	mr1490	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
vg0816293722	8.82E-06	NA	mr1023_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
vg0816293722	9.52E-09	NA	mr1055_2	Jap_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
vg0816293722	4.13E-07	NA	mr1132_2	Jap_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
vg0816293722	7.01E-06	NA	mr1390_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
vg0816293722	2.70E-06	NA	mr1490_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