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Detailed information for vg0137505966:

Variant ID: vg0137505966 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37505966
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCCGGCGGCCAGCACGAGACGCCTTAGCACCAACGTGACTCAACTGTACAGTAGGCTATCACAGTAGTTGGGAACACAGTGAACATTTTTTTGCTTT[T/C]
CTTTTGTCATCCGAGATACTGTGGTCATTATCTCTGTTTTTTTTTTCTTTTCTGTTATGTTCATGTCGAAGTGACCCGGTTCCGATGAAATGAAGGTGAA

Reverse complement sequence

TTCACCTTCATTTCATCGGAACCGGGTCACTTCGACATGAACATAACAGAAAAGAAAAAAAAAACAGAGATAATGACCACAGTATCTCGGATGACAAAAG[A/G]
AAAGCAAAAAAATGTTCACTGTGTTCCCAACTACTGTGATAGCCTACTGTACAGTTGAGTCACGTTGGTGCTAAGGCGTCTCGTGCTGGCCGCCGGCGGC

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 55.10% 44.70% 0.21% 0.04% NA
All Indica  2759 27.90% 71.90% 0.11% 0.07% NA
All Japonica  1512 97.80% 2.00% 0.20% 0.00% NA
Aus  269 74.30% 25.70% 0.00% 0.00% NA
Indica I  595 1.70% 98.00% 0.34% 0.00% NA
Indica II  465 16.60% 83.40% 0.00% 0.00% NA
Indica III  913 44.10% 55.90% 0.00% 0.00% NA
Indica Intermediate  786 35.50% 64.10% 0.13% 0.25% NA
Temperate Japonica  767 98.20% 1.70% 0.13% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.10% 0.83% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 68.90% 27.80% 3.33% 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
vg0137505966 T -> DEL N N silent_mutation Average:84.19; most accessible tissue: Callus, score: 91.795 N N N N
vg0137505966 T -> C LOC_Os01g64620.1 3_prime_UTR_variant ; 71.0bp to feature; MODIFIER silent_mutation Average:84.19; most accessible tissue: Callus, score: 91.795 N N N N
vg0137505966 T -> C LOC_Os01g64630.1 upstream_gene_variant ; 3919.0bp to feature; MODIFIER silent_mutation Average:84.19; most accessible tissue: Callus, score: 91.795 N N N N
vg0137505966 T -> C LOC_Os01g64630.2 upstream_gene_variant ; 3919.0bp to feature; MODIFIER silent_mutation Average:84.19; most accessible tissue: Callus, score: 91.795 N N N N
vg0137505966 T -> C LOC_Os01g64630.4 upstream_gene_variant ; 3919.0bp to feature; MODIFIER silent_mutation Average:84.19; most accessible tissue: Callus, score: 91.795 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0137505966 T C 0.04 0.01 0.02 0.03 0.05 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137505966 NA 4.80E-32 mr1213 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
vg0137505966 NA 4.96E-15 mr1583 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
vg0137505966 NA 1.55E-13 mr1592 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
vg0137505966 NA 9.19E-07 mr1717 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
vg0137505966 NA 7.50E-10 mr1770 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
vg0137505966 NA 1.75E-07 mr1215_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
vg0137505966 NA 2.18E-20 mr1218_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
vg0137505966 NA 3.32E-16 mr1352_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
vg0137505966 1.21E-06 NA mr1538_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
vg0137505966 NA 5.03E-13 mr1850_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
vg0137505966 NA 1.49E-06 mr1870_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
vg0137505966 NA 2.68E-07 mr1885_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