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Detailed information for vg0920044521:

Variant ID: vg0920044521 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20044521
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


TCTTGAGGTAAGCTATATTGTCTGTTTTAAGTTTGGTATCTGCATCTAATTTGGTCGGAAGAGTGTATCATTACATTTCTCTTCAGAGGATAAATTAATA[A/C]
TCTGTACCATCTTTGTTTCTCAGAAGGGAAGAATAAATCCATCGCCTGAAAAGAAAGCAGCAGCATCCCTTGTTGCCTTGCCCTCCTTGTTATCAAATGC

Reverse complement sequence

GCATTTGATAACAAGGAGGGCAAGGCAACAAGGGATGCTGCTGCTTTCTTTTCAGGCGATGGATTTATTCTTCCCTTCTGAGAAACAAAGATGGTACAGA[T/G]
TATTAATTTATCCTCTGAAGAGAAATGTAATGATACACTCTTCCGACCAAATTAGATGCAGATACCAAACTTAAAACAGACAATATAGCTTACCTCAAGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.10% 4.40% 1.57% 0.00% NA
All Indica  2759 90.00% 7.40% 2.61% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 77.50% 15.80% 6.72% 0.00% NA
Indica II  465 86.20% 9.50% 4.30% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 90.50% 8.00% 1.53% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 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
vg0920044521 A -> C LOC_Os09g33950.1 upstream_gene_variant ; 4120.0bp to feature; MODIFIER silent_mutation Average:61.603; most accessible tissue: Callus, score: 83.515 N N N N
vg0920044521 A -> C LOC_Os09g33960.1 intron_variant ; MODIFIER silent_mutation Average:61.603; most accessible tissue: Callus, score: 83.515 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920044521 NA 4.34E-06 mr1418 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
vg0920044521 2.70E-06 2.86E-06 mr1418 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