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Detailed information for vg1206301896:

Variant ID: vg1206301896 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 6301896
Reference Allele: TAlternative Allele: A,TGGATA
Primary Allele: TSecondary Allele: TGGATA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATGCTGTTGGTTGATTAAAAGTAAACTAATAACCAACGGCGTACAGCTTATAATCATGGCACAGTAGTAGGCGGTGGGCATGAATATTGGCCTGGAT[T/A,TGGATA]
GCAGGTCGGATACGGAGTCGGAAGCAGTCCACTTTGAAGCAACACCCTCGCGGCGGAGGCCATCACCGGCGCCTCCTGCAGCGCCGCCGCCATGACGAAC

Reverse complement sequence

GTTCGTCATGGCGGCGGCGCTGCAGGAGGCGCCGGTGATGGCCTCCGCCGCGAGGGTGTTGCTTCAAAGTGGACTGCTTCCGACTCCGTATCCGACCTGC[A/T,TATCCA]
ATCCAGGCCAATATTCATGCCCACCGCCTACTACTGTGCCATGATTATAAGCTGTACGCCGTTGGTTATTAGTTTACTTTTAATCAACCAACAGCATATA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of TGGATA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.90% 5.50% 2.07% 20.42% A: 0.15%
All Indica  2759 88.50% 5.10% 1.16% 5.11% A: 0.04%
All Japonica  1512 51.00% 0.70% 2.84% 45.50% NA
Aus  269 13.80% 37.90% 5.20% 42.38% A: 0.74%
Indica I  595 91.10% 0.80% 0.00% 8.07% NA
Indica II  465 95.30% 2.60% 1.08% 1.08% NA
Indica III  913 88.50% 7.40% 1.53% 2.41% A: 0.11%
Indica Intermediate  786 82.70% 7.30% 1.65% 8.40% NA
Temperate Japonica  767 60.80% 1.00% 4.04% 34.16% NA
Tropical Japonica  504 33.50% 0.20% 1.19% 65.08% NA
Japonica Intermediate  241 56.40% 0.40% 2.49% 40.66% NA
VI/Aromatic  96 86.50% 1.00% 6.25% 2.08% A: 4.17%
Intermediate  90 71.10% 3.30% 3.33% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1206301896 T -> TGGATA LOC_Os12g11620.1 frameshift_variant ; p.Asn56fs; HIGH frameshift_variant Average:69.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 N N N N
vg1206301896 T -> DEL LOC_Os12g11620.1 N frameshift_variant Average:69.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 N N N N
vg1206301896 T -> A LOC_Os12g11620.1 missense_variant ; p.Asn56Tyr; MODERATE nonsynonymous_codon Average:69.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.874 unknown unknown TOLERATED 0.22

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)
vg1206301896 T A 0.09 0.02 0.01 0.02 0.02 0.01
vg1206301896 T TGGAT* 0.23 0.02 0.03 0.03 0.05 0.05