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Detailed information for vg0816239139:

Variant ID: vg0816239139 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16239139
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGCAGAAGTATGTACTGCTCATGCATCTGTACTGTTCAGAAAACAAAATGTATTTTAGATAGGCTGGCAACAATCACGAGAACAATTCCACTTAAATT[G/T]
CTCTGTTGATCCCAAAGTTTCAGAACAAGAGCTAAATCTCAAGTAGAAAAAGCTCCTGGGAGAACTCAATGATGAAGAAAATACAAATGCAAAATATTTA

Reverse complement sequence

TAAATATTTTGCATTTGTATTTTCTTCATCATTGAGTTCTCCCAGGAGCTTTTTCTACTTGAGATTTAGCTCTTGTTCTGAAACTTTGGGATCAACAGAG[C/A]
AATTTAAGTGGAATTGTTCTCGTGATTGTTGCCAGCCTATCTAAAATACATTTTGTTTTCTGAACAGTACAGATGCATGAGCAGTACATACTTCTGCGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.50%	3.90%	0.83%	8.80%	NA
All Indica	2759	92.50%	6.30%	0.87%	0.25%	NA
All Japonica	1512	74.00%	0.20%	0.79%	25.00%	NA
Aus	269	90.00%	0.00%	1.12%	8.92%	NA
Indica I	595	98.50%	0.00%	1.18%	0.34%	NA
Indica II	465	92.70%	5.60%	1.29%	0.43%	NA
Indica III	913	88.10%	11.10%	0.77%	0.11%	NA
Indica Intermediate	786	93.10%	6.10%	0.51%	0.25%	NA
Temperate Japonica	767	97.80%	0.00%	0.13%	2.09%	NA
Tropical Japonica	504	49.40%	0.60%	1.98%	48.02%	NA
Japonica Intermediate	241	49.80%	0.00%	0.41%	49.79%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	90.00%	6.70%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816239139	G -> T	LOC_Os08g26700.1	missense_variant ; p.Gln121Lys; MODERATE	nonsynonymous_codon ; Q121K	Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 52.263	unknown	unknown	DELETERIOUS	0.00
vg0816239139	G -> DEL	LOC_Os08g26700.1	N	frameshift_variant	Average:36.569; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816239139	9.58E-07	3.01E-08	mr1090	Ind_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
vg0816239139	3.48E-06	NA	mr1111	Ind_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
vg0816239139	2.75E-06	1.36E-06	mr1121	Ind_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
vg0816239139	1.53E-06	5.03E-08	mr1211	Ind_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
vg0816239139	2.47E-07	NA	mr1068_2	Ind_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
vg0816239139	2.77E-09	4.68E-09	mr1090_2	Ind_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
vg0816239139	5.26E-07	NA	mr1094_2	Ind_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
vg0816239139	5.89E-06	NA	mr1096_2	Ind_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
vg0816239139	4.76E-07	NA	mr1111_2	Ind_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
vg0816239139	1.85E-07	2.66E-07	mr1121_2	Ind_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
vg0816239139	5.10E-07	NA	mr1144_2	Ind_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
vg0816239139	6.82E-09	5.94E-10	mr1211_2	Ind_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