Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0515524688:

Variant ID: vg0515524688 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15524688
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCCAGATTCCGATCAAAGTAGAGATCATCAAACTGCTGGAGTTGTAGCTGCTGCGCTATGACCTGAAAAATGTTAATATCCTCATAGTGAGACTGTTG[C/T]
GCCACCAGCCAAAGCTGTTGCCAGACTTGGTTGTTTCTCAGTTGAAACGCAACTGATTGCAATAAGGGGCTTGCCGTTATGCCATACTGCTGCCTTACGA

Reverse complement sequence

TCGTAAGGCAGCAGTATGGCATAACGGCAAGCCCCTTATTGCAATCAGTTGCGTTTCAACTGAGAAACAACCAAGTCTGGCAACAGCTTTGGCTGGTGGC[G/A]
CAACAGTCTCACTATGAGGATATTAACATTTTTCAGGTCATAGCGCAGCAGCTACAACTCCAGCAGTTTGATGATCTCTACTTTGATCGGAATCTGGCTC

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 56.00% 0.40% 4.59% 38.95% NA
All Indica  2759 42.80% 0.60% 5.04% 51.54% NA
All Japonica  1512 78.00% 0.30% 0.33% 21.43% NA
Aus  269 47.60% 0.00% 26.02% 26.39% NA
Indica I  595 26.20% 0.50% 1.18% 72.10% NA
Indica II  465 63.20% 0.20% 0.65% 35.91% NA
Indica III  913 48.70% 0.90% 9.53% 40.85% NA
Indica Intermediate  786 36.40% 0.60% 5.34% 57.63% NA
Temperate Japonica  767 94.30% 0.10% 0.13% 5.48% NA
Tropical Japonica  504 52.00% 0.60% 0.79% 46.63% NA
Japonica Intermediate  241 80.50% 0.00% 0.00% 19.50% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 70.00% 0.00% 3.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0515524688 C -> T LOC_Os05g26750.1 synonymous_variant ; p.Ala83Ala; LOW synonymous_codon Average:21.526; most accessible tissue: Callus, score: 39.575 N N N N
vg0515524688 C -> DEL LOC_Os05g26750.1 N frameshift_variant Average:21.526; most accessible tissue: Callus, score: 39.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515524688 5.88E-07 5.88E-07 mr1184 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
vg0515524688 NA 1.29E-07 mr1243 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
vg0515524688 NA 4.11E-06 mr1378 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
vg0515524688 NA 6.02E-08 mr1423 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
vg0515524688 NA 4.42E-07 mr1951 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