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Detailed information for vg0119596620:

Variant ID: vg0119596620 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 19596620
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGAGTACTCCTACAGCCGCTGTTTGAAGGCGTACTTGCTCTGGCTTTTTGGCTGGGTGATGTTCTGTTGCGGTCACGTGCACGCGGTCGACAAGGGTCT[T/C]
GTGCACTATGCCAGGAGCATCGCTGACGCCGCGGTTGGCGAGGTCCCTCAGTGGAGCTGGGGTTCCGCGTTGTTGGTGGCTCAGTACCGTGGCCTTTGTG

Reverse complement sequence

CACAAAGGCCACGGTACTGAGCCACCAACAACGCGGAACCCCAGCTCCACTGAGGGACCTCGCCAACCGCGGCGTCAGCGATGCTCCTGGCATAGTGCAC[A/G]
AGACCCTTGTCGACCGCGTGCACGTGACCGCAACAGAACATCACCCAGCCAAAAAGCCAGAGCAAGTACGCCTTCAAACAGCGGCTGTAGGAGTACTCGT

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 73.00% 5.60% 12.93% 8.44% NA
All Indica  2759 78.80% 0.40% 8.95% 11.92% NA
All Japonica  1512 61.50% 16.60% 21.23% 0.66% NA
Aus  269 69.10% 0.00% 10.04% 20.82% NA
Indica I  595 69.10% 0.00% 17.48% 13.45% NA
Indica II  465 66.20% 1.50% 13.33% 18.92% NA
Indica III  913 95.00% 0.10% 0.66% 4.27% NA
Indica Intermediate  786 74.70% 0.30% 9.54% 15.52% NA
Temperate Japonica  767 38.70% 30.40% 30.77% 0.13% NA
Tropical Japonica  504 92.10% 0.40% 7.34% 0.20% NA
Japonica Intermediate  241 70.10% 6.60% 19.92% 3.32% NA
VI/Aromatic  96 96.90% 0.00% 3.12% 0.00% NA
Intermediate  90 77.80% 3.30% 14.44% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0119596620 T -> DEL LOC_Os01g35420.1 N frameshift_variant Average:72.06; most accessible tissue: Zhenshan97 young leaf, score: 89.772 N N N N
vg0119596620 T -> C LOC_Os01g35420.1 synonymous_variant ; p.Leu305Leu; LOW synonymous_codon Average:72.06; most accessible tissue: Zhenshan97 young leaf, score: 89.772 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)
vg0119596620 T C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0119596620 NA 2.20E-07 mr1164 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
vg0119596620 NA 1.02E-06 mr1205 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