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Detailed information for vg0106807221:

Variant ID: vg0106807221 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6807221
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GATAGTATAAACGTAGTACTCCCTCCGTCAAAAAAAAAACAACTATACAAGAATACTCCCTCCGTCCAAAAAAAGACAAACCCTAGGTTTCCATGCTCAA[C/T]
GTTTGACTGTTCGTCTTATATGAAATTTTTTTATAATTAGTATTTTTATTGTTGTTAGATGATAAAACATGATTAATATTTTATGTGTGACTTATCTTTT

Reverse complement sequence

AAAAGATAAGTCACACATAAAATATTAATCATGTTTTATCATCTAACAACAATAAAAATACTAATTATAAAAAAATTTCATATAAGACGAACAGTCAAAC[G/A]
TTGAGCATGGAAACCTAGGGTTTGTCTTTTTTTGGACGGAGGGAGTATTCTTGTATAGTTGTTTTTTTTTTGACGGAGGGAGTACTACGTTTATACTATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.40% 22.50% 1.95% 1.10% NA
All Indica  2759 71.20% 28.10% 0.62% 0.07% NA
All Japonica  1512 74.70% 17.30% 4.83% 3.17% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 87.20% 12.80% 0.00% 0.00% NA
Indica II  465 54.00% 45.80% 0.00% 0.22% NA
Indica III  913 82.30% 17.20% 0.44% 0.11% NA
Indica Intermediate  786 56.50% 41.90% 1.65% 0.00% NA
Temperate Japonica  767 96.90% 2.60% 0.52% 0.00% NA
Tropical Japonica  504 46.80% 33.10% 12.50% 7.54% NA
Japonica Intermediate  241 62.70% 30.70% 2.49% 4.15% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 67.80% 27.80% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106807221 C -> T LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:60.855; most accessible tissue: Callus, score: 94.1 N N N N
vg0106807221 C -> DEL N N silent_mutation Average:60.855; most accessible tissue: Callus, score: 94.1 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106807221 NA 4.48E-10 mr1017 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
vg0106807221 NA 1.40E-09 mr1022 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
vg0106807221 NA 4.88E-08 mr1236 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
vg0106807221 NA 3.68E-09 mr1518 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
vg0106807221 NA 9.30E-10 mr1676 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
vg0106807221 NA 1.04E-07 mr1746 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
vg0106807221 6.90E-06 NA mr1769 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
vg0106807221 1.15E-18 4.01E-33 mr1769 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
vg0106807221 NA 7.43E-07 mr1925 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
vg0106807221 2.95E-06 2.72E-12 mr1951 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
vg0106807221 NA 4.93E-06 mr1389_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
vg0106807221 6.39E-13 1.04E-15 mr1498_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
vg0106807221 NA 4.37E-09 mr1676_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
vg0106807221 1.29E-07 NA mr1769_2 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
vg0106807221 4.65E-27 2.25E-47 mr1769_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
vg0106807221 NA 7.97E-11 mr1916_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
vg0106807221 8.41E-09 1.08E-09 mr1951_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