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Detailed information for vg0616957969:

Variant ID: vg0616957969 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 16957969
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AGATACCCCGCTGATTGATTACATGCCCTAGGAAAACCACCTCAGGAAGCCAAAATTCACACTTCTTTAATTTAGCATAGAACTTGTTTTCCCGTAAAGT[C/T]
CCTAGCACCATCCTTAAATGATGCTTATGCTCATCTACATCTTTGGAGTAAATCAGAATATCATGAATAAACACCACCACAAACTTATCTAGAAAGCTAT

Reverse complement sequence

ATAGCTTTCTAGATAAGTTTGTGGTGGTGTTTATTCATGATATTCTGATTTACTCCAAAGATGTAGATGAGCATAAGCATCATTTAAGGATGGTGCTAGG[G/A]
ACTTTACGGGAAAACAAGTTCTATGCTAAATTAAAGAAGTGTGAATTTTGGCTTCCTGAGGTGGTTTTCCTAGGGCATGTAATCAATCAGCGGGGTATCT

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	67.80%	6.20%	1.69%	24.35%	NA
All Indica	2759	57.10%	0.70%	2.79%	39.40%	NA
All Japonica	1512	87.90%	10.60%	0.13%	1.32%	NA
Aus	269	81.00%	7.10%	0.37%	11.52%	NA
Indica I	595	88.60%	0.00%	1.18%	10.25%	NA
Indica II	465	83.90%	1.50%	0.43%	14.19%	NA
Indica III	913	17.20%	0.80%	4.82%	77.22%	NA
Indica Intermediate	786	63.70%	0.80%	3.05%	32.44%	NA
Temperate Japonica	767	98.00%	0.30%	0.26%	1.43%	NA
Tropical Japonica	504	70.60%	28.00%	0.00%	1.39%	NA
Japonica Intermediate	241	91.70%	7.50%	0.00%	0.83%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	14.40%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0616957969	C -> T	LOC_Os06g29580.1	synonymous_variant ; p.Gly203Gly; LOW	synonymous_codon	Average:41.578; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N
vg0616957969	C -> DEL	LOC_Os06g29580.1	N	frameshift_variant	Average:41.578; most accessible tissue: Zhenshan97 young leaf, score: 63.096	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0616957969	6.14E-06	NA	mr1086	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
vg0616957969	1.27E-06	NA	mr1436	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
vg0616957969	NA	2.28E-06	mr1930	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
vg0616957969	2.86E-08	NA	mr1082_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
vg0616957969	5.75E-09	NA	mr1083_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
vg0616957969	2.75E-07	NA	mr1085_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
vg0616957969	2.56E-06	NA	mr1103_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
vg0616957969	4.63E-06	NA	mr1104_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
vg0616957969	8.80E-06	NA	mr1107_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
vg0616957969	1.72E-06	NA	mr1145_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
vg0616957969	1.49E-06	NA	mr1226_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
vg0616957969	1.49E-07	4.56E-09	mr1408_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
vg0616957969	NA	1.45E-06	mr1408_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