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Detailed information for vg0327535213:

Variant ID: vg0327535213 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27535213
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


GTCGCCGGGAGATCTAGTCGAACCAACTCGATTACGATCTCGCCGGTTTCATCGAGTTCCATCGTTCCCTTTGTAACCTGTGGTTTTCCATCATATAATC[C/T]
CATATCAACTGAATTAGGGCTATTACCTATTAAGGGGCCTGAACCAGTATAATCCTCGTCTTTTGTTTGCTCGATGTCGTATTACGTAGATCCTTGTACC

Reverse complement sequence

GGTACAAGGATCTACGTAATACGACATCGAGCAAACAAAAGACGAGGATTATACTGGTTCAGGCCCCTTAATAGGTAATAGCCCTAATTCAGTTGATATG[G/A]
GATTATATGATGGAAAACCACAGGTTACAAAGGGAACGATGGAACTCGATGAAACCGGCGAGATCGTAATCGAGTTGGTTCGACTAGATCTCCCGGCGAC

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 97.40% 1.00% 1.57% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.40% 2.80% 4.76% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 86.60% 4.70% 8.74% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 2.50% 2.07% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 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
vg0327535213 C -> T LOC_Os03g48364.1 missense_variant ; p.Pro115Leu; MODERATE nonsynonymous_codon ; P115L Average:56.425; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327535213 1.92E-06 NA mr1310 Jap_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
vg0327535213 2.20E-06 NA mr1926 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