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Detailed information for vg0416188668:

Variant ID: vg0416188668 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16188668
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTATTTTGGCACCAATATCATTTGCTGCCCACTCAAATGCTTCGTTCGTTAGTGCATCACCTCGACCGACTGTAGTAGACACACATAGTAGTGGCACGGT[T/C]
GAGGTTACCGTAGACAAAGCCACTTGCTCTTCAAAGCTTGGCTTGTAATTCTGATATGACCATTCCGCTTCTTGAAGATAATAAGCAGATAGATTTTGGA

Reverse complement sequence

TCCAAAATCTATCTGCTTATTATCTTCAAGAAGCGGAATGGTCATATCAGAATTACAAGCCAAGCTTTGAAGAGCAAGTGGCTTTGTCTACGGTAACCTC[A/G]
ACCGTGCCACTACTATGTGTGTCTACTACAGTCGGTCGAGGTGATGCACTAACGAACGAAGCATTTGAGTGGGCAGCAAATGATATTGGTGCCAAAATAG

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 76.30% 23.60% 0.06% 0.00% NA
All Indica  2759 75.00% 24.90% 0.07% 0.00% NA
All Japonica  1512 90.50% 9.50% 0.07% 0.00% NA
Aus  269 3.70% 96.30% 0.00% 0.00% NA
Indica I  595 89.20% 10.60% 0.17% 0.00% NA
Indica II  465 79.80% 20.20% 0.00% 0.00% NA
Indica III  913 59.80% 40.20% 0.00% 0.00% NA
Indica Intermediate  786 79.00% 20.90% 0.13% 0.00% NA
Temperate Japonica  767 99.20% 0.70% 0.13% 0.00% NA
Tropical Japonica  504 74.00% 26.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 0.00% 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
vg0416188668 T -> C LOC_Os04g27400.1 synonymous_variant ; p.Ser360Ser; LOW synonymous_codon Average:34.66; most accessible tissue: Zhenshan97 young leaf, score: 69.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416188668 3.59E-06 9.48E-06 mr1925 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
vg0416188668 8.66E-06 1.37E-06 mr1043_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
vg0416188668 NA 8.04E-06 mr1269_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
vg0416188668 2.83E-06 2.83E-06 mr1730_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
vg0416188668 9.88E-06 3.92E-06 mr1866_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
vg0416188668 1.66E-07 1.66E-07 mr1912_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