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Detailed information for vg0817080070:

Variant ID: vg0817080070 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17080070
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTTTCAAAATGTTGATGCATTCCACACTTGGCATGATCGACTTGGGCACCCCGGTATCGAGATGATGAGAAAAATTATTGGCAACTCTATTGGTCAT[C/T]
ATTTGATCACTGACAAATTTCCAAAATCCTCTGATTTCGTATGCACTGCATGTGCTACTGGGAAACTGATTTTGAGACCATCTTATCTCAAAATTAGAGC

Reverse complement sequence

GCTCTAATTTTGAGATAAGATGGTCTCAAAATCAGTTTCCCAGTAGCACATGCAGTGCATACGAAATCAGAGGATTTTGGAAATTTGTCAGTGATCAAAT[G/A]
ATGACCAATAGAGTTGCCAATAATTTTTCTCATCATCTCGATACCGGGGTGCCCAAGTCGATCATGCCAAGTGTGGAATGCATCAACATTTTGAAAAATT

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 67.60% 32.00% 0.47% 0.00% NA
All Indica  2759 46.20% 53.10% 0.69% 0.00% NA
All Japonica  1512 98.90% 1.00% 0.07% 0.00% NA
Aus  269 97.40% 2.20% 0.37% 0.00% NA
Indica I  595 75.50% 24.20% 0.34% 0.00% NA
Indica II  465 12.30% 86.70% 1.08% 0.00% NA
Indica III  913 41.70% 57.80% 0.44% 0.00% NA
Indica Intermediate  786 49.40% 49.60% 1.02% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 72.20% 26.70% 1.11% 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
vg0817080070 C -> T LOC_Os08g28040.1 missense_variant ; p.His182Tyr; MODERATE nonsynonymous_codon ; H182Y Average:19.163; most accessible tissue: Zhenshan97 panicle, score: 24.575 unknown unknown TOLERATED 0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817080070 NA 8.99E-06 mr1319 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
vg0817080070 NA 9.97E-06 mr1319 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
vg0817080070 NA 2.98E-06 mr1330 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
vg0817080070 NA 3.38E-12 mr1336 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
vg0817080070 NA 2.25E-09 mr1336 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
vg0817080070 NA 8.42E-06 mr1579 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
vg0817080070 NA 1.54E-06 mr1701 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