Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0601621819:

Variant ID: vg0601621819 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 1621819
Reference Allele: AAlternative Allele: G,ATTAGGGTTTAGGGTTTAGGGTTTAGGG,ATTAGGGTTTAGGG,ATTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACCTGTGCTGTTGCTGCGCATGCATGATCATCATGAGCACACCAGCGGACCAGCCTTGTGAAACATCTGTCCTATAAAGAACAAATTTCTCACGTTCAG[A/G,ATTAGGGTTTAGGGTTTAGGGTTTAGGG,ATTAGGGTTTAGGG,ATTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG]
TTCATTGATAACAGATGATACCGTTGACTTTTTTTAACATATTTGACTATTTATCTTATTCAAAAATTTTATGCAAATGTATAAGATATAAATCACACTT

Reverse complement sequence

AAGTGTGATTTATATCTTATACATTTGCATAAAATTTTTGAATAAGATAAATAGTCAAATATGTTAAAAAAAGTCAACGGTATCATCTGTTATCAATGAA[T/C,CCCTAAACCCTAAACCCTAAACCCTAAT,CCCTAAACCCTAAT,CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAT]
CTGAACGTGAGAAATTTGTTCTTTATAGGACAGATGTTTCACAAGGCTGGTCCGCTGGTGTGCTCATGATGATCATGCATGCGCAGCAACAGCACAGGTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.90% 6.60% 0.04% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 3.32%; ATTAGGGTTTAGGG: 0.08%; ATTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG: 0.06%
All Indica  2759 96.00% 1.70% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 2.14%; ATTAGGGTTTAGGG: 0.11%
All Japonica  1512 86.60% 13.20% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 0.26%
Aus  269 63.60% 0.40% 0.74% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 33.83%; ATTAGGGTTTAGGGTTTAGGGTTTAGGGTTTAGGG: 1.12%; ATTAGGGTTTAGGG: 0.37%
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 91.80% 6.00% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 2.15%
Indica III  913 96.30% 0.30% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 3.07%; ATTAGGGTTTAGGG: 0.33%
Indica Intermediate  786 95.30% 2.00% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 2.67%
Temperate Japonica  767 99.50% 0.30% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 0.26%
Tropical Japonica  504 67.50% 32.30% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 0.20%
Japonica Intermediate  241 85.50% 14.10% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 0.41%
VI/Aromatic  96 50.00% 47.90% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 2.08%
Intermediate  90 78.90% 20.00% 0.00% 0.00% ATTAGGGTTTAGGGTTTAGGGTTTAGGG: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0601621819 A -> G LOC_Os06g03980.1 upstream_gene_variant ; 1636.0bp to feature; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> G LOC_Os06g03980-LOC_Os06g03990 intergenic_region ; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGGTTTAGGGTTTAGGG LOC_Os06g03980.1 upstream_gene_variant ; 1637.0bp to feature; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGGTTTAGGGTTTAGGG LOC_Os06g03980-LOC_Os06g03990 intergenic_region ; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGG LOC_Os06g03980.1 upstream_gene_variant ; 1637.0bp to feature; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGG LOC_Os06g03980-LOC_Os06g03990 intergenic_region ; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGGTTTAGGGTTTAGGGTT TAGGG LOC_Os06g03980.1 upstream_gene_variant ; 1637.0bp to feature; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 N N N N
vg0601621819 A -> ATTAGGGTTTAGGGTTTAGGGTTTAGGGTT TAGGG LOC_Os06g03980-LOC_Os06g03990 intergenic_region ; MODIFIER silent_mutation Average:85.312; most accessible tissue: Minghui63 panicle, score: 96.976 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)
vg0601621819 A ATTAG* 0.25 -0.07 -0.1 0.26 0.09 0.06
vg0601621819 A G 0.02 0.0 0.0 -0.01 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0601621819 NA 2.85E-06 mr1852 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
vg0601621819 2.61E-06 NA mr1040_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
vg0601621819 6.42E-06 NA mr1070_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
vg0601621819 6.62E-06 NA mr1083_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
vg0601621819 6.62E-06 NA mr1104_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
vg0601621819 8.82E-07 NA mr1107_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
vg0601621819 3.62E-06 NA mr1208_2 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
vg0601621819 1.59E-06 NA mr1226_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
vg0601621819 NA 3.27E-06 mr1227_2 Jap_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
vg0601621819 NA 4.24E-08 mr1408_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
vg0601621819 NA 2.14E-06 mr1707_2 Jap_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
vg0601621819 1.83E-06 NA mr1846_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
vg0601621819 2.37E-06 2.37E-06 mr1846_2 Jap_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
vg0601621819 NA 4.19E-06 mr1852_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