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Detailed information for vg0113686887:

Variant ID: vg0113686887 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13686887
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


TTATAACCAAATGCTTAGTGTATCAAACTATTGGACCAAAATCCCTCCTCTCTAGACATATGAAAAATTATAACATCCAACTAACATGTCTAGATGAATA[T/C]
TAATTCAAATGGCTTTTGAAACAATAATCATCATGGCATCAAAACACTTAGCCAATTGAAGTATGATCAATAATGAATCACCAAAGTCATATGTGTCACA

Reverse complement sequence

TGTGACACATATGACTTTGGTGATTCATTATTGATCATACTTCAATTGGCTAAGTGTTTTGATGCCATGATGATTATTGTTTCAAAAGCCATTTGAATTA[A/G]
TATTCATCTAGACATGTTAGTTGGATGTTATAATTTTTCATATGTCTAGAGAGGAGGGATTTTGGTCCAATAGTTTGATACACTAAGCATTTGGTTATAA

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 53.80% 35.30% 2.18% 8.74% NA
All Indica  2759 85.20% 9.60% 1.67% 3.44% NA
All Japonica  1512 2.10% 86.60% 1.92% 9.39% NA
Aus  269 21.20% 10.80% 5.95% 62.08% NA
Indica I  595 74.30% 18.70% 1.51% 5.55% NA
Indica II  465 90.50% 4.90% 2.37% 2.15% NA
Indica III  913 92.70% 3.60% 1.64% 2.08% NA
Indica Intermediate  786 81.80% 12.60% 1.40% 4.20% NA
Temperate Japonica  767 0.80% 97.80% 0.00% 1.43% NA
Tropical Japonica  504 4.60% 66.70% 4.96% 23.81% NA
Japonica Intermediate  241 1.20% 92.50% 1.66% 4.56% NA
VI/Aromatic  96 62.50% 27.10% 10.42% 0.00% NA
Intermediate  90 46.70% 41.10% 2.22% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113686887 T -> DEL N N silent_mutation Average:16.381; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 N N N N
vg0113686887 T -> C LOC_Os01g24294.1 intron_variant ; MODIFIER silent_mutation Average:16.381; most accessible tissue: Zhenshan97 flag leaf, score: 30.355 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113686887 NA 2.19E-42 mr1136 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
vg0113686887 NA 4.73E-11 mr1175 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
vg0113686887 NA 6.05E-06 mr1188 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
vg0113686887 NA 2.53E-10 mr1316 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
vg0113686887 NA 3.48E-31 mr1448 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
vg0113686887 NA 1.94E-07 mr1741 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
vg0113686887 3.23E-06 NA mr1136_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
vg0113686887 NA 8.00E-06 mr1457_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
vg0113686887 NA 6.07E-09 mr1458_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