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Detailed information for vg0826622371:

Variant ID: vg0826622371 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26622371
Reference Allele: CAlternative Allele: T
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:


CGCTTGCGCCCTAACTCCTTCTTTCCTGTGCCCTACCTTCGCCACACGCGCTCGCTCTCAAACATCTCTTCTTCCGGCGTCATGGCACGGGGCTCCGCTC[C/T]
GCTCGATGGTAGCATGCTGCCGCCTTCCCGCATCGTGAGCGAGAGGCAGGTCAGGCTGCCACGCCGCTTCATGCCGGAATCTGCCACCGGCCGGGAGATA

Reverse complement sequence

TATCTCCCGGCCGGTGGCAGATTCCGGCATGAAGCGGCGTGGCAGCCTGACCTGCCTCTCGCTCACGATGCGGGAAGGCGGCAGCATGCTACCATCGAGC[G/A]
GAGCGGAGCCCCGTGCCATGACGCCGGAAGAAGAGATGTTTGAGAGCGAGCGCGTGTGGCGAAGGTAGGGCACAGGAAAGAAGGAGTTAGGGCGCAAGCG

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 34.70% 19.00% 39.80% 6.54% NA
All Indica  2759 7.40% 31.20% 57.92% 3.55% NA
All Japonica  1512 82.60% 0.30% 3.51% 13.62% NA
Aus  269 17.10% 8.60% 73.23% 1.12% NA
Indica I  595 4.20% 38.20% 48.57% 9.08% NA
Indica II  465 6.20% 45.80% 47.10% 0.86% NA
Indica III  913 10.80% 17.30% 69.33% 2.52% NA
Indica Intermediate  786 6.40% 33.30% 58.14% 2.16% NA
Temperate Japonica  767 94.80% 0.00% 1.69% 3.52% NA
Tropical Japonica  504 72.60% 0.40% 4.96% 22.02% NA
Japonica Intermediate  241 64.70% 0.80% 6.22% 28.22% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 51.10% 12.20% 34.44% 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
vg0826622371 C -> T LOC_Os08g42130.1 missense_variant ; p.Pro7Leu; MODERATE nonsynonymous_codon ; P7L Average:15.112; most accessible tissue: Minghui63 root, score: 23.574 unknown unknown TOLERATED 1.00
vg0826622371 C -> DEL LOC_Os08g42130.1 N frameshift_variant Average:15.112; most accessible tissue: Minghui63 root, score: 23.574 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826622371 NA 7.61E-12 mr1070 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
vg0826622371 NA 1.64E-10 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
vg0826622371 NA 2.11E-06 mr1184_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
vg0826622371 NA 2.69E-06 mr1278_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
vg0826622371 NA 3.35E-20 mr1336_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
vg0826622371 NA 5.53E-06 mr1336_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
vg0826622371 NA 1.30E-18 mr1579_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
vg0826622371 NA 4.04E-07 mr1579_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
vg0826622371 NA 6.33E-21 mr1627_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
vg0826622371 NA 1.32E-07 mr1683_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
vg0826622371 NA 1.01E-08 mr1690_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