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Detailed information for vg0810146037:

Variant ID: vg0810146037 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 10146037
Reference Allele: AAlternative Allele: ATG,G,ACG
Primary Allele: GSecondary Allele: ATG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATAAAAAGAAAAACTAATTGCATAGTTTGTATGTAAATTGTGAGACGAATCTTTTGAGCCTAATTAGTCTATGATTAATCATACTACAGTAACCCATAT[A/ATG,G,ACG]
TGCTAATGACGGATTAATCATGAAATTAATTTTTTCATTCGTGCCCGAAAACTTCTTCCGATATCCGGTCCAACGTCCGATGCGACACCTTAAAATTTTC

Reverse complement sequence

GAAAATTTTAAGGTGTCGCATCGGACGTTGGACCGGATATCGGAAGAAGTTTTCGGGCACGAATGAAAAAATTAATTTCATGATTAATCCGTCATTAGCA[T/CAT,C,CGT]
ATATGGGTTACTGTAGTATGATTAATCATAGACTAATTAGGCTCAAAAGATTCGTCTCACAATTTACATACAAACTATGCAATTAGTTTTTCTTTTTATC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of ATG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.80% 39.70% 0.30% 0.28% A: 12.93%; ACG: 0.02%
All Indica  2759 36.50% 61.10% 0.40% 0.43% A: 1.56%; ACG: 0.04%
All Japonica  1512 62.10% 1.60% 0.07% 0.00% A: 36.24%
Aus  269 49.80% 49.40% 0.37% 0.00% A: 0.37%
Indica I  595 17.80% 76.50% 0.67% 0.34% A: 4.71%
Indica II  465 54.60% 43.90% 0.86% 0.00% A: 0.65%
Indica III  913 40.50% 58.60% 0.00% 0.66% A: 0.22%
Indica Intermediate  786 35.20% 62.50% 0.38% 0.51% A: 1.27%; ACG: 0.13%
Temperate Japonica  767 36.10% 1.70% 0.13% 0.00% A: 62.06%
Tropical Japonica  504 91.70% 1.00% 0.00% 0.00% A: 7.34%
Japonica Intermediate  241 83.00% 2.50% 0.00% 0.00% A: 14.52%
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 46.70% 30.00% 1.11% 1.11% A: 21.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810146037 A -> G LOC_Os08g16580.1 upstream_gene_variant ; 1260.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> G LOC_Os08g16570.1 downstream_gene_variant ; 4312.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> G LOC_Os08g16590.1 downstream_gene_variant ; 1877.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> G LOC_Os08g16570.3 downstream_gene_variant ; 4312.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> G LOC_Os08g16580-LOC_Os08g16590 intergenic_region ; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ACG LOC_Os08g16580.1 upstream_gene_variant ; 1261.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ACG LOC_Os08g16570.1 downstream_gene_variant ; 4313.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ACG LOC_Os08g16590.1 downstream_gene_variant ; 1876.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ACG LOC_Os08g16570.3 downstream_gene_variant ; 4313.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ACG LOC_Os08g16580-LOC_Os08g16590 intergenic_region ; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ATG LOC_Os08g16580.1 upstream_gene_variant ; 1261.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ATG LOC_Os08g16570.1 downstream_gene_variant ; 4313.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ATG LOC_Os08g16590.1 downstream_gene_variant ; 1876.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ATG LOC_Os08g16570.3 downstream_gene_variant ; 4313.0bp to feature; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> ATG LOC_Os08g16580-LOC_Os08g16590 intergenic_region ; MODIFIER silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 N N N N
vg0810146037 A -> DEL N N silent_mutation Average:90.199; most accessible tissue: Zhenshan97 root, score: 94.906 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)
vg0810146037 A ACG -0.07 -0.27 -0.14 -0.03 0.03 0.15
vg0810146037 A ATG -0.11 -0.28 -0.14 -0.03 0.03 0.15
vg0810146037 A G -0.02 -0.02 -0.01 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810146037 NA 2.42E-06 mr1057 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
vg0810146037 NA 6.91E-10 mr1182 Jap_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
vg0810146037 NA 8.18E-06 mr1202 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
vg0810146037 NA 1.79E-08 mr1282 Jap_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
vg0810146037 NA 4.92E-07 mr1330 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
vg0810146037 NA 4.43E-07 mr1510 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
vg0810146037 NA 2.96E-07 mr1627 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
vg0810146037 NA 2.77E-08 mr1650 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
vg0810146037 NA 2.35E-07 mr1658 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
vg0810146037 NA 1.49E-07 mr1057_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
vg0810146037 NA 1.23E-11 mr1057_2 Jap_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
vg0810146037 NA 3.60E-07 mr1182_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
vg0810146037 NA 9.24E-06 mr1282_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
vg0810146037 NA 6.14E-08 mr1627_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
vg0810146037 NA 2.02E-06 mr1980_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