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Detailed information for vg0429731545:

Variant ID: vg0429731545 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29731545
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCACGCTGCGGTGCGTGAAGCACTGGGCCAAGGCGCGGGGCGTCTACTCCAACGTCGCGGGCTTCCTCGGCGGCGTCGGCTGGGCCATCCTCGTGGCG[T/C]
GCGTGTGCTTGCTCTACCCCAACGCCTCCCCCAGCATGCTGCTCCCGCGCTTCTTCCGCGTCTTCGCGCGGTGGAAGTGGCCCAGCCCGGTGATGCTGCG

Reverse complement sequence

CGCAGCATCACCGGGCTGGGCCACTTCCACCGCGCGAAGACGCGGAAGAAGCGCGGGAGCAGCATGCTGGGGGAGGCGTTGGGGTAGAGCAAGCACACGC[A/G]
CGCCACGAGGATGGCCCAGCCGACGCCGCCGAGGAAGCCCGCGACGTTGGAGTAGACGCCCCGCGCCTTGGCCCAGTGCTTCACGCACCGCAGCGTGGTG

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 85.40% 14.40% 0.15% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 58.10% 41.50% 0.40% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.40% 0.00% 0.00% NA
Temperate Japonica  767 74.40% 25.00% 0.52% 0.00% NA
Tropical Japonica  504 23.60% 76.40% 0.00% 0.00% NA
Japonica Intermediate  241 78.40% 20.70% 0.83% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 1.11% 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
vg0429731545 T -> C LOC_Os04g49870.1 missense_variant ; p.Cys245Arg; MODERATE nonsynonymous_codon ; C245R Average:89.313; most accessible tissue: Zhenshan97 panicle, score: 94.949 benign -0.724 TOLERATED 1.00

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)
vg0429731545 T C 0.02 0.02 0.03 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429731545 NA 2.74E-06 mr1121 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
vg0429731545 NA 2.82E-06 mr1121_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
vg0429731545 NA 6.53E-06 mr1319_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
vg0429731545 NA 7.54E-07 mr1781_2 Jap_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