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Detailed information for vg0813872533:

Variant ID: vg0813872533 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13872533
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GCACCGAGCCAGGCAGATGCGAGACGTATCTGCCAGATTCCAGGAGCCGCTCAGAGGGACCTGGTGACGAGCAGGAGGACGCCTTCGACTCCACCGACCG[C/T]
AGGAGCCGTTCCGAGCATTAGGCTCGCTTTCCATTAGTTTATCGACTATTTAGCATTTGCCTGTTAGTTTGTGTGTTTAGGTCTGCTCGCTTGTGGGTCA

Reverse complement sequence

TGACCCACAAGCGAGCAGACCTAAACACACAAACTAACAGGCAAATGCTAAATAGTCGATAAACTAATGGAAAGCGAGCCTAATGCTCGGAACGGCTCCT[G/A]
CGGTCGGTGGAGTCGAAGGCGTCCTCCTGCTCGTCACCAGGTCCCTCTGAGCGGCTCCTGGAATCTGGCAGATACGTCTCGCATCTGCCTGGCTCGGTGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.60%	4.50%	0.17%	0.63%	NA
All Indica	2759	91.00%	7.60%	0.29%	1.09%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	97.60%	2.20%	0.00%	0.17%	NA
Indica II	465	95.30%	4.10%	0.22%	0.43%	NA
Indica III	913	83.80%	13.10%	0.77%	2.30%	NA
Indica Intermediate	786	91.70%	7.50%	0.00%	0.76%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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	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
vg0813872533	C -> T	LOC_Os08g23040.1	synonymous_variant ; p.Arg249Arg; LOW	synonymous_codon	Average:67.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N
vg0813872533	C -> DEL	LOC_Os08g23040.1	N	frameshift_variant	Average:67.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.17	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813872533	1.00E-07	1.85E-10	mr1238	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
vg0813872533	7.29E-08	2.91E-09	mr1309	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
vg0813872533	8.02E-06	8.74E-07	mr1484	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
vg0813872533	3.57E-09	2.61E-11	mr1841	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
vg0813872533	3.05E-08	3.05E-08	mr1900	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
vg0813872533	4.16E-07	3.25E-10	mr1238_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
vg0813872533	3.92E-07	1.41E-09	mr1484_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
vg0813872533	2.17E-06	3.83E-11	mr1841_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
vg0813872533	1.95E-06	1.16E-09	mr1900_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
vg0813872533	2.91E-06	2.91E-06	mr1945_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