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Detailed information for vg0821203177:

Variant ID: vg0821203177 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21203177
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCCTTCTTATCTAATTCATCTGCCTTTGCTAGCAAGCTAGCCTTTTCTTTCTTGTAGGCCCCACTTGTATCTTTTGCCCAACCTCTCAAAAATTGACG[C/T]
AGCCTTCGTAACCTATTTTGCCACTTTTCCAACCTTGTAACCCCCCTAACCTCCTTTTTCCAAACATCCGCTACCATATCATAGAATCCATCTCTTAACA

Reverse complement sequence

TGTTAAGAGATGGATTCTATGATATGGTAGCGGATGTTTGGAAAAAGGAGGTTAGGGGGGTTACAAGGTTGGAAAAGTGGCAAAATAGGTTACGAAGGCT[G/A]
CGTCAATTTTTGAGAGGTTGGGCAAAAGATACAAGTGGGGCCTACAAGAAAGAAAAGGCTAGCTTGCTAGCAAAGGCAGATGAATTAGATAAGAAGGCTG

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	90.90%	0.60%	7.09%	1.46%	NA
All Indica	2759	95.30%	0.30%	3.55%	0.83%	NA
All Japonica	1512	80.70%	1.10%	15.15%	3.04%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.50%	0.50%	1.68%	0.34%	NA
Indica II	465	97.40%	0.00%	2.15%	0.43%	NA
Indica III	913	92.10%	0.10%	6.13%	1.64%	NA
Indica Intermediate	786	96.20%	0.50%	2.80%	0.51%	NA
Temperate Japonica	767	97.50%	0.00%	2.35%	0.13%	NA
Tropical Japonica	504	56.20%	3.00%	32.74%	8.13%	NA
Japonica Intermediate	241	78.40%	0.80%	19.09%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	1.10%	8.89%	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
vg0821203177	C -> T	LOC_Os08g33870.1	synonymous_variant ; p.Leu348Leu; LOW	synonymous_codon	Average:37.182; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0821203177	C -> DEL	LOC_Os08g33870.1	N	frameshift_variant	Average:37.182; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821203177	NA	1.88E-16	mr1301	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
vg0821203177	NA	1.16E-13	mr1410	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
vg0821203177	NA	6.10E-12	mr1980	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
vg0821203177	NA	4.42E-07	mr1993	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
vg0821203177	3.87E-06	NA	mr1064_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
vg0821203177	NA	2.13E-16	mr1301_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
vg0821203177	NA	4.46E-13	mr1410_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
vg0821203177	NA	2.04E-11	mr1533_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
vg0821203177	NA	2.80E-07	mr1578_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