Search for Variation information by Variation ID:

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

Detailed information for vg0138752753:

Variant ID: vg0138752753 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38752753
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACCCAAACGGCAAGCGGCAGTGCCAATGGAGCAGCAACAGGCGGCGCCCATGGCGAGGAACAGGAAGGTGGTGCTGCGCGAGTACATCGCCGGCCGG[C/T]
CGCCGAGGGAGGACGACATGGTGCTCGTCGACGGCGGCACGGTGGCCCTGCGCGTGCCGGAGGCCGCCGCCCCCGCCCCGGCGGTCCTCGTGAAGAATCT

Reverse complement sequence

AGATTCTTCACGAGGACCGCCGGGGCGGGGGCGGCGGCCTCCGGCACGCGCAGGGCCACCGTGCCGCCGTCGACGAGCACCATGTCGTCCTCCCTCGGCG[G/A]
CCGGCCGGCGATGTACTCGCGCAGCACCACCTTCCTGTTCCTCGCCATGGGCGCCGCCTGTTGCTGCTCCATTGGCACTGCCGCTTGCCGTTTGGGTGGT

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 59.50% 39.90% 0.04% 0.49% NA
All Indica  2759 36.80% 62.30% 0.07% 0.83% NA
All Japonica  1512 93.10% 6.90% 0.00% 0.00% NA
Aus  269 90.70% 9.30% 0.00% 0.00% NA
Indica I  595 59.20% 40.00% 0.00% 0.84% NA
Indica II  465 3.70% 96.10% 0.00% 0.22% NA
Indica III  913 45.20% 53.70% 0.11% 0.99% NA
Indica Intermediate  786 29.50% 69.30% 0.13% 1.02% NA
Temperate Japonica  767 97.30% 2.70% 0.00% 0.00% NA
Tropical Japonica  504 86.10% 13.90% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg0138752753 C -> T LOC_Os01g66720.1 missense_variant ; p.Pro25Ser; MODERATE nonsynonymous_codon ; P25S Average:97.403; most accessible tissue: Zhenshan97 panicle, score: 99.024 benign 1.16 TOLERATED 0.50
vg0138752753 C -> DEL LOC_Os01g66720.1 N frameshift_variant Average:97.403; most accessible tissue: Zhenshan97 panicle, score: 99.024 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)
vg0138752753 C T -0.05 -0.06 -0.04 -0.04 -0.03 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138752753 NA 7.40E-06 mr1163 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
vg0138752753 NA 2.04E-10 mr1720 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
vg0138752753 NA 9.83E-06 mr1062_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
vg0138752753 NA 4.62E-06 mr1265_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
vg0138752753 NA 2.26E-06 mr1360_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
vg0138752753 NA 2.12E-06 mr1946_2 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
vg0138752753 NA 2.12E-06 mr1948_2 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