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Detailed information for vg0209506636:

Variant ID: vg0209506636 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 9506636
Reference Allele: GAlternative Allele: GTTC
Primary Allele: GSecondary Allele: GTTC

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGGAGCACCAGGATAACCTGAGGAGCGTACAGAGAAGTCACATAAATAATATACTCGTTATTTGGTTTGATCAAGTGAAATGGATTAATAAGTGGAAA[G/GTTC]
AACATCAGTCCATGATTAGCGTGCATTTTCTGTAAGTGTATGCAATGGCAAAATGATAACATTAGCAGTAGCGTTCCTTTGGTAAGTGGTAGCTCATCTT

Reverse complement sequence

AAGATGAGCTACCACTTACCAAAGGAACGCTACTGCTAATGTTATCATTTTGCCATTGCATACACTTACAGAAAATGCACGCTAATCATGGACTGATGTT[C/GAAC]
TTTCCACTTATTAATCCATTTCACTTGATCAAACCAAATAACGAGTATATTATTTATGTGACTTCTCTGTACGCTCCTCAGGTTATCCTGGTGCTCCAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GTTC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.90% 18.00% 0.02% 0.00% NA
All Indica  2759 70.00% 30.00% 0.04% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 57.50% 42.50% 0.00% 0.00% NA
Indica II  465 58.10% 41.90% 0.00% 0.00% NA
Indica III  913 90.70% 9.30% 0.00% 0.00% NA
Indica Intermediate  786 62.50% 37.40% 0.13% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 0.00% 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
vg0209506636 G -> GTTC LOC_Os02g16650.1 upstream_gene_variant ; 3365.0bp to feature; MODIFIER silent_mutation Average:84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg0209506636 G -> GTTC LOC_Os02g16630.1 downstream_gene_variant ; 1175.0bp to feature; MODIFIER silent_mutation Average:84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg0209506636 G -> GTTC LOC_Os02g16630.2 downstream_gene_variant ; 1175.0bp to feature; MODIFIER silent_mutation Average:84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg0209506636 G -> GTTC LOC_Os02g16640.1 intron_variant ; MODIFIER silent_mutation Average:84.658; most accessible tissue: Zhenshan97 panicle, score: 93.752 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)
vg0209506636 G GTTC -0.02 -0.07 0.0 -0.02 0.03 0.02