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Detailed information for vg0418998438:

Variant ID: vg0418998438 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 18998438
Reference Allele: AAlternative Allele: AT,ATT,ATTT,ATTTT
Primary Allele: ASecondary Allele: AT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACCTGCCTCCCCAAAAGGTTTTTTACTCCCCGATCAAATCGAAGTTTAGTGAACTCGAATCCGAAGATATCAAGAGCAGAGCTGTGATTTTTGGTTTGG[A/AT,ATT,ATTT,ATTTT]
TTTATTTTTTTTTGGTTTTACCACTTGGAATGGCGGCTGGACATGGGACTTGCACATGATGCAGGTGAAGTAGGGCTTCCCGAGGAGTGGGAGCACCCCG

Reverse complement sequence

CGGGGTGCTCCCACTCCTCGGGAAGCCCTACTTCACCTGCATCATGTGCAAGTCCCATGTCCAGCCGCCATTCCAAGTGGTAAAACCAAAAAAAAATAAA[T/AT,AAT,AAAT,AAAAT]
CCAAACCAAAAATCACAGCTCTGCTCTTGATATCTTCGGATTCGAGTTCACTAAACTTCGATTTGATCGGGGAGTAAAAAACCTTTTGGGGAGGCAGGTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of AT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.80% 19.80% 4.53% 0.00% ATT: 4.23%; ATTT: 1.57%; ATTTT: 0.02%
All Indica  2759 51.60% 33.50% 6.81% 0.00% ATT: 5.51%; ATTT: 2.57%; ATTTT: 0.04%
All Japonica  1512 99.90% 0.10% 0.07% 0.00% NA
Aus  269 71.70% 3.30% 7.43% 0.00% ATT: 16.36%; ATTT: 1.12%
Indica I  595 45.50% 41.30% 12.27% 0.00% ATT: 0.84%
Indica II  465 83.90% 10.10% 1.94% 0.00% ATT: 4.09%
Indica III  913 36.00% 42.10% 4.60% 0.00% ATT: 9.75%; ATTT: 7.45%; ATTTT: 0.11%
Indica Intermediate  786 55.20% 31.30% 8.14% 0.00% ATT: 4.96%; ATTT: 0.38%
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 85.60% 5.60% 4.44% 0.00% ATT: 4.44%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0418998438 A -> ATTTT LOC_Os04g31740.1 upstream_gene_variant ; 2912.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTTT LOC_Os04g31710.1 downstream_gene_variant ; 2748.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTTT LOC_Os04g31720.1 downstream_gene_variant ; 1863.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTTT LOC_Os04g31730.1 intron_variant ; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTT LOC_Os04g31740.1 upstream_gene_variant ; 2912.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTT LOC_Os04g31710.1 downstream_gene_variant ; 2748.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTT LOC_Os04g31720.1 downstream_gene_variant ; 1863.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATTT LOC_Os04g31730.1 intron_variant ; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATT LOC_Os04g31740.1 upstream_gene_variant ; 2912.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATT LOC_Os04g31710.1 downstream_gene_variant ; 2748.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATT LOC_Os04g31720.1 downstream_gene_variant ; 1863.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> ATT LOC_Os04g31730.1 intron_variant ; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> AT LOC_Os04g31740.1 upstream_gene_variant ; 2912.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> AT LOC_Os04g31710.1 downstream_gene_variant ; 2748.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> AT LOC_Os04g31720.1 downstream_gene_variant ; 1863.0bp to feature; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 N N N N
vg0418998438 A -> AT LOC_Os04g31730.1 intron_variant ; MODIFIER silent_mutation Average:79.238; most accessible tissue: Minghui63 panicle, score: 92.526 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)
vg0418998438 A AT 0.09 0.05 0.0 0.15 0.11 0.07
vg0418998438 A ATT 0.11 0.03 -0.01 0.11 0.1 0.07
vg0418998438 A ATTT 0.03 -0.02 -0.05 -0.02 -0.02 -0.06
vg0418998438 A ATTTT -0.04 -0.11 -0.2 -0.05 -0.11 -0.16