Search for Variation information by Variation ID:

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

Detailed information for vg0134942609:

Variant ID: vg0134942609 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 34942609
Reference Allele: TCAlternative Allele: AC,TTTTTCGGTGC,TTTTCGGGTGC,T
Primary Allele: ACSecondary Allele: TC

Inferred Ancestral Allele : TC (evidence from allele frequency in Oryza rufipogon: TC: 1.00, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGGTTATCTTAACCTGGTGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCACCTTTT[TC/AC,TTTTTCGGTGC,TTTTCGGGTGC,T]
TTTTGTACTCACTCACTCAGCAGCGCCATTAATCATGAGCAGAAACACAAACAGCCAAAAGGACGAGCCAACTACTAGACAATACAAAAAGCAACAGTCG

Reverse complement sequence

CGACTGTTGCTTTTTGTATTGTCTAGTAGTTGGCTCGTCCTTTTGGCTGTTTGTGTTTCTGCTCATGATTAATGGCGCTGCTGAGTGAGTGAGTACAAAA[GA/GT,GCACCGAAAAA,GCACCCGAAAA,A]
AAAAGGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGGCCACCAGGTTAAGATAACCTAT

Allele Frequencies:

Populations Population SizeFrequency of AC(primary allele) Frequency of TC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.50% 41.70% 1.10% 1.65% T: 0.04%
All Indica  2759 92.30% 4.20% 1.05% 2.46% NA
All Japonica  1512 1.90% 96.50% 1.06% 0.53% NA
Aus  269 2.60% 97.00% 0.37% 0.00% NA
Indica I  595 91.10% 5.00% 2.35% 1.51% NA
Indica II  465 92.90% 1.50% 1.29% 4.30% NA
Indica III  913 95.80% 1.80% 0.22% 2.19% NA
Indica Intermediate  786 88.80% 7.90% 0.89% 2.42% NA
Temperate Japonica  767 1.60% 98.30% 0.00% 0.13% NA
Tropical Japonica  504 2.40% 93.70% 2.78% 1.19% NA
Japonica Intermediate  241 2.10% 96.70% 0.83% 0.41% NA
VI/Aromatic  96 7.30% 89.60% 2.08% 1.04% NA
Intermediate  90 34.40% 57.80% 4.44% 1.11% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0134942609 TC -> T LOC_Os01g60420.1 upstream_gene_variant ; 1198.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> T LOC_Os01g60430.1 upstream_gene_variant ; 4008.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> T LOC_Os01g60410.1 downstream_gene_variant ; 614.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> T LOC_Os01g60410.3 downstream_gene_variant ; 614.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> T LOC_Os01g60410.2 downstream_gene_variant ; 614.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> T LOC_Os01g60410-LOC_Os01g60420 intergenic_region ; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60420.1 upstream_gene_variant ; 1198.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60430.1 upstream_gene_variant ; 4008.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60410.1 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60410.3 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60410.2 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTTCGGTGC LOC_Os01g60410-LOC_Os01g60420 intergenic_region ; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> DEL N N silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60420.1 upstream_gene_variant ; 1198.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60430.1 upstream_gene_variant ; 4008.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60410.1 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60410.3 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60410.2 downstream_gene_variant ; 614.0bp to feature; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> TTTTCGGGTGC LOC_Os01g60410-LOC_Os01g60420 intergenic_region ; MODIFIER N Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60420.1 upstream_gene_variant ; 1199.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60430.1 upstream_gene_variant ; 4009.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60410.1 downstream_gene_variant ; 613.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60410.3 downstream_gene_variant ; 613.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60410.2 downstream_gene_variant ; 613.0bp to feature; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 N N N N
vg0134942609 TC -> AC LOC_Os01g60410-LOC_Os01g60420 intergenic_region ; MODIFIER silent_mutation Average:99.077; most accessible tissue: Zhenshan97 root, score: 99.84 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)
vg0134942609 TC AC 0.0 -0.04 -0.04 -0.02 -0.05 -0.07
vg0134942609 TC T 0.21 0.21 0.15 0.05 0.09 0.1
vg0134942609 TC TTTTC* -0.03 -0.01 0.12 0.09 0.14 0.16
vg0134942609 TC TTTTT* -0.01 -0.03 0.12 0.08 0.14 0.16

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134942609 NA 4.30E-22 mr1003 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
vg0134942609 4.72E-09 NA mr1008 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
vg0134942609 1.25E-09 6.51E-15 mr1008 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
vg0134942609 5.16E-09 NA mr1009 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
vg0134942609 6.61E-10 1.05E-14 mr1009 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
vg0134942609 NA 1.28E-12 mr1010 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
vg0134942609 NA 1.18E-07 mr1014 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
vg0134942609 NA 1.27E-06 mr1015 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
vg0134942609 NA 9.87E-07 mr1038 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
vg0134942609 NA 3.96E-09 mr1047 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
vg0134942609 NA 9.75E-23 mr1051 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
vg0134942609 NA 2.45E-18 mr1179 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
vg0134942609 NA 6.11E-06 mr1189 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
vg0134942609 NA 1.70E-29 mr1208 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
vg0134942609 NA 2.04E-10 mr1316 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
vg0134942609 NA 2.64E-12 mr1744 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
vg0134942609 NA 2.07E-32 mr1745 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
vg0134942609 NA 5.76E-30 mr1793 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
vg0134942609 NA 1.09E-06 mr1796 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
vg0134942609 NA 1.81E-11 mr1883 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
vg0134942609 1.06E-07 NA mr1008_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
vg0134942609 1.27E-09 2.32E-15 mr1008_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
vg0134942609 NA 8.00E-07 mr1015_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
vg0134942609 NA 5.07E-26 mr1051_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
vg0134942609 NA 2.24E-13 mr1151_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
vg0134942609 NA 2.91E-12 mr1189_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
vg0134942609 NA 2.72E-34 mr1221_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
vg0134942609 NA 7.04E-26 mr1244_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
vg0134942609 NA 6.22E-27 mr1270_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
vg0134942609 NA 3.42E-07 mr1389_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
vg0134942609 NA 1.14E-24 mr1422_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
vg0134942609 NA 1.76E-07 mr1527_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
vg0134942609 NA 8.63E-06 mr1677_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
vg0134942609 NA 3.73E-15 mr1744_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
vg0134942609 NA 1.25E-44 mr1793_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
vg0134942609 NA 2.32E-06 mr1834_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
vg0134942609 NA 3.28E-34 mr1932_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
vg0134942609 NA 2.09E-61 mr1970_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