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Detailed information for vg0111725377:

Variant ID: vg0111725377 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11725377
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.57, T: 0.41, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


CTATCACCTCCTTACGCGTGTCGCTGGCCGCCCCCTGGTCCAAGATCTCGCGCAGATCGAGTTCAGGACGCGACAGTCTTACACACACGAGGACATGACA[T/C]
GCCCCGGTGTAGATCCCGTTCGACGTCTCCTCCGCGATCCTGGCCGCATGCTTGGAGGGGATTTCCCCCATCACTGTCGCCAGTTCCGCGAGAGAGGAGG

Reverse complement sequence

CCTCCTCTCTCGCGGAACTGGCGACAGTGATGGGGGAAATCCCCTCCAAGCATGCGGCCAGGATCGCGGAGGAGACGTCGAACGGGATCTACACCGGGGC[A/G]
TGTCATGTCCTCGTGTGTGTAAGACTGTCGCGTCCTGAACTCGATCTGCGCGAGATCTTGGACCAGGGGGCGGCCAGCGACACGCGTAAGGAGGTGATAG

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 66.90% 33.00% 0.06% 0.00% NA
All Indica  2759 98.50% 1.40% 0.07% 0.00% NA
All Japonica  1512 3.20% 96.80% 0.00% 0.00% NA
Aus  269 97.00% 2.60% 0.37% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 98.10% 1.80% 0.13% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0111725377 T -> C LOC_Os01g21000.1 synonymous_variant ; p.Ala24Ala; LOW synonymous_codon Average:42.027; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111725377 NA 3.90E-39 mr1480 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
vg0111725377 NA 1.15E-25 mr1617 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
vg0111725377 8.05E-06 NA mr1778 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
vg0111725377 NA 1.04E-16 mr1968 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
vg0111725377 NA 5.28E-15 mr1162_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
vg0111725377 NA 8.41E-35 mr1223_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
vg0111725377 NA 5.08E-06 mr1355_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
vg0111725377 NA 3.71E-07 mr1668_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
vg0111725377 NA 2.29E-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
vg0111725377 NA 7.72E-16 mr1836_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