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Detailed information for vg0820534605:

Variant ID: vg0820534605 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 20534605
Reference Allele: TCAlternative Allele: AC,T
Primary Allele: TCSecondary Allele: AC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATCAGATTGACCTCCCTGTATTCTTTCCTTAATATACTACACTGACTGACCGTGTACATATATCCGTGTTGGATGTATAGGCCGGGTTTCAATCCATCA[TC/AC,T]
CAAAAAAACATATACTACACTGACATTCAGTTTAATTTCTTTCCTTTATAACTTACATGGTATATATTACTGTTTTATAAACTACACTGACACACATAAA

Reverse complement sequence

TTTATGTGTGTCAGTGTAGTTTATAAAACAGTAATATATACCATGTAAGTTATAAAGGAAAGAAATTAAACTGAATGTCAGTGTAGTATATGTTTTTTTG[GA/GT,A]
TGATGGATTGAAACCCGGCCTATACATCCAACACGGATATATGTACACGGTCAGTCAGTGTAGTATATTAAGGAAAGAATACAGGGAGGTCAATCTGATG

Allele Frequencies:

Populations Population SizeFrequency of TC(primary allele) Frequency of AC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.10% 26.70% 0.17% 0.00% T: 0.04%
All Indica  2759 60.70% 39.10% 0.22% 0.00% NA
All Japonica  1512 97.80% 2.20% 0.00% 0.00% NA
Aus  269 46.50% 53.50% 0.00% 0.00% NA
Indica I  595 60.50% 39.00% 0.50% 0.00% NA
Indica II  465 88.80% 11.00% 0.22% 0.00% NA
Indica III  913 42.10% 57.90% 0.00% 0.00% NA
Indica Intermediate  786 65.90% 33.80% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 94.00% 6.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 0.00% 0.00% T: 2.08%
Intermediate  90 88.90% 8.90% 2.22% 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
vg0820534605 TC -> T LOC_Os08g33060.1 upstream_gene_variant ; 4265.0bp to feature; MODIFIER silent_mutation Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N
vg0820534605 TC -> T LOC_Os08g33050.1 intron_variant ; MODIFIER silent_mutation Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N
vg0820534605 TC -> AC LOC_Os08g33060.1 upstream_gene_variant ; 4266.0bp to feature; MODIFIER silent_mutation Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 86.383 N N N N
vg0820534605 TC -> AC LOC_Os08g33050.1 intron_variant ; MODIFIER silent_mutation Average:70.949; most accessible tissue: Zhenshan97 young leaf, score: 86.383 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)
vg0820534605 TC AC 0.0 0.0 0.01 -0.01 -0.02 -0.01
vg0820534605 TC T -0.03 -0.05 -0.03 0.0 -0.11 -0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0820534605 6.74E-07 6.74E-07 mr1153_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 8.06E-07 mr1252_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 2.81E-10 mr1388_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 1.08E-07 mr1388_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 7.67E-09 mr1482_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 8.40E-06 mr1528_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 9.58E-06 mr1545_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 5.40E-06 mr1659_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 1.15E-06 mr1702_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 4.10E-06 mr1702_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 5.97E-06 mr1785_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0820534605 NA 3.03E-06 mr1943_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251