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Detailed information for vg0619755654:

Variant ID: vg0619755654 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 19755654
Reference Allele: T	Alternative Allele: C
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TAACCTTAAATTTGGAGCTGATTTTGTGTTTTTTTCATAGAAGTTTATTTTTCAGCCTTTGCTTTTAGATCGCTAAGAACACATATATAAAAGTTGTATT[T/C]
ATAAATTACTTTTCATTTGCAAATATGTCATTTCGCTTATTTCGCGAATAAGCGAAACAATGGCTCCTGTAGTTTTCAGCGTATATTTTCCCTGCTAAGC

Reverse complement sequence

GCTTAGCAGGGAAAATATACGCTGAAAACTACAGGAGCCATTGTTTCGCTTATTCGCGAAATAAGCGAAATGACATATTTGCAAATGAAAAGTAATTTAT[A/G]
AATACAACTTTTATATATGTGTTCTTAGCGATCTAAAAGCAAAGGCTGAAAAATAAACTTCTATGAAAAAAACACAAAATCAGCTCCAAATTTAAGGTTA

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	50.40%	49.20%	0.38%	0.00%	NA
All Indica	2759	60.60%	39.10%	0.33%	0.00%	NA
All Japonica	1512	20.70%	78.90%	0.40%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	92.60%	7.10%	0.34%	0.00%	NA
Indica II	465	71.00%	28.80%	0.22%	0.00%	NA
Indica III	913	33.20%	66.60%	0.22%	0.00%	NA
Indica Intermediate	786	62.00%	37.50%	0.51%	0.00%	NA
Temperate Japonica	767	27.90%	71.40%	0.65%	0.00%	NA
Tropical Japonica	504	11.50%	88.50%	0.00%	0.00%	NA
Japonica Intermediate	241	17.00%	82.60%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	43.30%	54.40%	2.22%	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
vg0619755654	T -> C	LOC_Os06g33940-LOC_Os06g33950	intergenic_region ; MODIFIER	silent_mutation	Average:37.339; most accessible tissue: Zhenshan97 flower, score: 62.865	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0619755654	NA	4.15E-06	mr1071	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
vg0619755654	NA	4.52E-06	mr1140	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
vg0619755654	NA	1.05E-06	mr1203	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
vg0619755654	NA	1.81E-09	mr1062_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
vg0619755654	NA	1.19E-06	mr1167_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
vg0619755654	NA	3.64E-06	mr1333_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
vg0619755654	NA	9.28E-08	mr1456_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
vg0619755654	NA	1.31E-06	mr1530_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
vg0619755654	NA	1.14E-07	mr1582_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
vg0619755654	NA	1.89E-08	mr1623_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
vg0619755654	5.49E-06	1.27E-08	mr1623_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
vg0619755654	NA	4.43E-06	mr1667_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
vg0619755654	NA	8.04E-06	mr1726_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
vg0619755654	NA	8.46E-07	mr1734_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
vg0619755654	NA	4.92E-06	mr1879_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