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Detailed information for vg0104648042:

Variant ID: vg0104648042 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 4648042
Reference Allele: GTAlternative Allele: G
Primary Allele: GTSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCAAACAAACCAACAAAAATAAAAAAGAAAAACAAGATTCAGTTTTTAGGTGTATAGGAGGAGCTTCTCCATTTTTTGTCGGAAATGGAGCAGTGAACA[GT/G]
TTTTCGCTTTATCGTCAGGAGGGACAGGAAAGTTCAGAGTCCTAGTAGTCTCAAAGTAACATTAGTTTCTTGGTTGGATTTTCGATTGATTTGGTTCTTT

Reverse complement sequence

AAAGAACCAAATCAATCGAAAATCCAACCAAGAAACTAATGTTACTTTGAGACTACTAGGACTCTGAACTTTCCTGTCCCTCCTGACGATAAAGCGAAAA[AC/C]
TGTTCACTGCTCCATTTCCGACAAAAAATGGAGAAGCTCCTCCTATACACCTAAAAACTGAATCTTGTTTTTCTTTTTTATTTTTGTTGGTTTGTTTGGT

Allele Frequencies:

Populations Population SizeFrequency of GT(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.70% 49.10% 0.17% 0.02% NA
All Indica  2759 19.50% 80.30% 0.14% 0.00% NA
All Japonica  1512 96.40% 3.40% 0.20% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 33.30% 66.40% 0.34% 0.00% NA
Indica II  465 5.80% 93.80% 0.43% 0.00% NA
Indica III  913 19.90% 80.10% 0.00% 0.00% NA
Indica Intermediate  786 16.80% 83.20% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 93.30% 6.20% 0.60% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 56.70% 41.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0104648042 GT -> G LOC_Os01g09220.1 3_prime_UTR_variant ; 145.0bp to feature; MODIFIER silent_mutation Average:95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 N N N N
vg0104648042 GT -> G LOC_Os01g09206.1 upstream_gene_variant ; 4933.0bp to feature; MODIFIER silent_mutation Average:95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 N N N N
vg0104648042 GT -> G LOC_Os01g09212.1 upstream_gene_variant ; 3347.0bp to feature; MODIFIER silent_mutation Average:95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 N N N N
vg0104648042 GT -> G LOC_Os01g09230.1 upstream_gene_variant ; 2052.0bp to feature; MODIFIER silent_mutation Average:95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 N N N N
vg0104648042 GT -> DEL N N silent_mutation Average:95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 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)
vg0104648042 GT G 0.05 0.03 -0.01 0.05 0.08 0.12