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Detailed information for vg0627917507:

Variant ID: vg0627917507 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 27917507
Reference Allele: GAAlternative Allele: GAA,GAAA,G
Primary Allele: GASecondary Allele: GAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCATATATACTACAAATCACAAATTCCAAAACAAATCACAAATTCCTAAACAAATCACAAATTCATATAATATATATTTATATACAAATCAACATAGA[GA/GAA,GAAA,G]
AAAAAAAGAAAAATAACAAAGAAATAGGAAAAAAAAGGTCTCCGGCACGCGCCGGGCTAGCCGTCGCATCCAGTGCCGCCGTGGAGCTTGCCTCCCGCCG

Reverse complement sequence

CGGCGGGAGGCAAGCTCCACGGCGGCACTGGATGCGACGGCTAGCCCGGCGCGTGCCGGAGACCTTTTTTTTCCTATTTCTTTGTTATTTTTCTTTTTTT[TC/TTC,TTTC,C]
TCTATGTTGATTTGTATATAAATATATATTATATGAATTTGTGATTTGTTTAGGAATTTGTGATTTGTTTTGGAATTTGTGATTTGTAGTATATATGAAT

Allele Frequencies:

Populations Population SizeFrequency of GA(primary allele) Frequency of GAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.50% 6.80% 3.36% 0.28% GAAA: 0.02%; G: 0.02%
All Indica  2759 89.10% 7.10% 3.81% 0.00% GAAA: 0.04%
All Japonica  1512 95.60% 0.70% 2.78% 0.86% G: 0.07%
Aus  269 55.80% 40.10% 4.09% 0.00% NA
Indica I  595 97.50% 0.20% 2.35% 0.00% NA
Indica II  465 83.90% 13.50% 2.58% 0.00% NA
Indica III  913 86.70% 7.70% 5.48% 0.00% GAAA: 0.11%
Indica Intermediate  786 88.50% 7.80% 3.69% 0.00% NA
Temperate Japonica  767 93.40% 0.40% 4.56% 1.69% NA
Tropical Japonica  504 98.00% 1.20% 0.79% 0.00% NA
Japonica Intermediate  241 97.50% 0.80% 1.24% 0.00% G: 0.41%
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 93.30% 5.60% 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
vg0627917507 GA -> GAAA LOC_Os06g46050.1 upstream_gene_variant ; 1461.0bp to feature; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> GAAA LOC_Os06g46050-LOC_Os06g46060 intergenic_region ; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> G LOC_Os06g46050.1 upstream_gene_variant ; 1460.0bp to feature; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> G LOC_Os06g46050-LOC_Os06g46060 intergenic_region ; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> GAA LOC_Os06g46050.1 upstream_gene_variant ; 1461.0bp to feature; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> GAA LOC_Os06g46050-LOC_Os06g46060 intergenic_region ; MODIFIER silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 N N N N
vg0627917507 GA -> DEL N N silent_mutation Average:78.157; most accessible tissue: Minghui63 flower, score: 97.761 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)
vg0627917507 GA G -0.03 -0.02 -0.05 -0.01 -0.04 -0.04
vg0627917507 GA GAA -0.07 -0.04 -0.04 -0.07 -0.04 -0.03
vg0627917507 GA GAAA -0.06 -0.04 -0.03 -0.06 -0.03 -0.01