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Detailed information for vg0318955179:

Variant ID: vg0318955179 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18955179
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGTGCCGAGCCCGCCCCCGTTGTTCCTCAGGAGGATGGAGCCTCCGGCGTTGGCAGCACAGAGGATGCGTTGCTGCTCACCTTCCGCCCTGGCCCGTCG[T/C]
AGCAGTAGACGAGCAGTTAGTAGGCTTGCGCGTGTGTTCTTCTCGTTTGTTTTTCTGCTAGAGTCATATAGGGCATGGTTATGCCGGTGTGTGGTATAAC

Reverse complement sequence

GTTATACCACACACCGGCATAACCATGCCCTATATGACTCTAGCAGAAAAACAAACGAGAAGAACACACGCGCAAGCCTACTAACTGCTCGTCTACTGCT[A/G]
CGACGGGCCAGGGCGGAAGGTGAGCAGCAACGCATCCTCTGTGCTGCCAACGCCGGAGGCTCCATCCTCCTGAGGAACAACGGGGGCGGGCTCGGCACGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.50% 0.90% 24.61% 37.03% NA
All Indica  2759 10.90% 1.40% 32.69% 55.02% NA
All Japonica  1512 86.40% 0.10% 2.38% 11.11% NA
Aus  269 13.80% 1.50% 68.40% 16.36% NA
Indica I  595 7.90% 0.20% 16.13% 75.80% NA
Indica II  465 6.90% 1.30% 27.53% 64.30% NA
Indica III  913 13.30% 2.30% 48.52% 35.93% NA
Indica Intermediate  786 12.80% 1.30% 29.90% 55.98% NA
Temperate Japonica  767 99.70% 0.00% 0.00% 0.26% NA
Tropical Japonica  504 66.90% 0.20% 2.58% 30.36% NA
Japonica Intermediate  241 85.10% 0.00% 9.54% 5.39% NA
VI/Aromatic  96 74.00% 0.00% 22.92% 3.12% NA
Intermediate  90 60.00% 0.00% 21.11% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318955179 T -> C LOC_Os03g33130.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:11.997; most accessible tissue: Callus, score: 43.337 N N N N
vg0318955179 T -> DEL LOC_Os03g33130.1 N splice_donor_variant Average:11.997; most accessible tissue: Callus, score: 43.337 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318955179 NA 3.10E-06 mr1215 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
vg0318955179 NA 3.89E-12 mr1386 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
vg0318955179 7.93E-08 4.56E-14 mr1750 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
vg0318955179 NA 1.06E-12 mr1751 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
vg0318955179 NA 2.22E-06 mr1751 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
vg0318955179 2.99E-08 8.37E-19 mr1750_2 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