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Detailed information for vg0816275999:

Variant ID: vg0816275999 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16275999
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGGGTATAAAACTAAATCCGGAAAAGTGTGGTTTTGGTGTTCACGCGGGCAAGTTGCTGGGTTTTCTTATTTCCTAAAGGGGTATCGAGGCGAACCCC[A/G]
AGAAAATCGATGCCATTCAGCAAATGAAGCCCCCATCGAGCGTACTCGAAGTACAAAAGGTCGCAGGCCGAATTGCGGCACTCAGTCGATTCCTCTCAAA

Reverse complement sequence

TTTGAGAGGAATCGACTGAGTGCCGCAATTCGGCCTGCGACCTTTTGTACTTCGAGTACGCTCGATGGGGGCTTCATTTGCTGAATGGCATCGATTTTCT[T/C]
GGGGTTCGCCTCGATACCCCTTTAGGAAATAAGAAAACCCAGCAACTTGCCCGCGTGAACACCAAAACCACACTTTTCCGGATTTAGTTTTATACCCGCG

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	43.70%	40.10%	10.20%	5.99%	NA
All Indica	2759	67.30%	20.80%	11.27%	0.58%	NA
All Japonica	1512	8.10%	74.70%	1.32%	15.87%	NA
Aus	269	23.40%	16.00%	52.79%	7.81%	NA
Indica I	595	40.20%	43.90%	15.13%	0.84%	NA
Indica II	465	67.30%	21.90%	10.54%	0.22%	NA
Indica III	913	88.40%	3.40%	7.78%	0.44%	NA
Indica Intermediate	786	63.40%	23.00%	12.85%	0.76%	NA
Temperate Japonica	767	0.50%	98.60%	0.00%	0.91%	NA
Tropical Japonica	504	21.40%	37.90%	2.98%	37.70%	NA
Japonica Intermediate	241	4.10%	75.90%	2.07%	17.84%	NA
VI/Aromatic	96	2.10%	95.80%	1.04%	1.04%	NA
Intermediate	90	22.20%	63.30%	8.89%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816275999	A -> G	LOC_Os08g26770.1	missense_variant ; p.Lys216Glu; MODERATE	nonsynonymous_codon ; K216E	Average:16.753; most accessible tissue: Callus, score: 53.972	benign	-0.278	TOLERATED	1.00
vg0816275999	A -> DEL	LOC_Os08g26770.1	N	frameshift_variant	Average:16.753; most accessible tissue: Callus, score: 53.972	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816275999	NA	3.96E-13	Grain_thickness	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
vg0816275999	NA	1.44E-06	mr1082	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
vg0816275999	NA	3.51E-06	mr1083	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
vg0816275999	NA	5.59E-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
vg0816275999	NA	2.12E-24	mr1217	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
vg0816275999	NA	2.61E-22	mr1300	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
vg0816275999	NA	2.23E-14	mr1376	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
vg0816275999	NA	2.58E-06	mr1424	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
vg0816275999	NA	2.23E-14	mr1431	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
vg0816275999	NA	7.21E-06	mr1681	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
vg0816275999	NA	4.19E-22	mr1845	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
vg0816275999	NA	6.00E-06	mr1884	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
vg0816275999	NA	6.73E-07	mr1077_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
vg0816275999	NA	6.42E-08	mr1526_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
vg0816275999	NA	2.39E-07	mr1952_2	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