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Detailed information for vg1204690369:

Variant ID: vg1204690369 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 4690369
Reference Allele: GAlternative Allele: A,GCGTACGTTTTCCAAACTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCACATGTTCTTTCCCCAACTTTTTCAACTTCTACTTGTTTTTCA
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCCAAGGAGCAATGTCCTTTTGAAAAAAAAAAACTGACCACAGTCGTACATTTAGACTGTGTTCTTTCCCCCAACTTTTTCAACTTCTACTTGTTTTTC[G/A,GCGTACGTTTTCCAAACTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCACATGTTCTTTCCCCAACTTTTTCAACTTCTACTTGTTTTTCA]
CGCGTACGTTTCCCAAATTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCATATGAACTCATTTTTCAAGTTTTT

Reverse complement sequence

AAAAACTTGAAAAATGAGTTCATATGATTTTTAAAAGTAACTTTCATATATAAAGTTTTTCTAAAAATTACACCATCTAGCAATTTGGGAAACGTACGCG[C/T,TGAAAAACAAGTAGAAGTTGAAAAAGTTGGGGAAAGAACATGTGATTTTTAAAAGTAACTTTCATATATAAAGTTTTTCTAAAAATTACACCATCTAGCAGTTTGGAAAACGTACGC]
GAAAAACAAGTAGAAGTTGAAAAAGTTGGGGGAAAGAACACAGTCTAAATGTACGACTGTGGTCAGTTTTTTTTTTTCAAAAGGACATTGCTCCTTGGCC

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 60.50% 38.00% 1.18% 0.17% GCGTACGTTTTCCAAACTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCACATGTTCTTTCCCCAACTTTTTCAACTTCTACTTGTTTTTCA: 0.08%
All Indica  2759 93.00% 4.90% 1.74% 0.29% GCGTACGTTTTCCAAACTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCACATGTTCTTTCCCCAACTTTTTCAACTTCTACTTGTTTTTCA: 0.14%
All Japonica  1512 12.80% 87.00% 0.20% 0.00% NA
Aus  269 26.40% 73.20% 0.37% 0.00% NA
Indica I  595 96.10% 1.80% 1.85% 0.17% NA
Indica II  465 95.50% 4.10% 0.43% 0.00% NA
Indica III  913 94.00% 2.70% 2.30% 0.55% GCGTACGTTTTCCAAACTGCTAGATGGTGTAATTTTTAGAAAAACTTTATATATGAAAGTTACTTTTAAAAATCACATGTTCTTTCCCCAACTTTTTCAACTTCTACTTGTTTTTCA: 0.44%
Indica Intermediate  786 87.90% 10.10% 1.78% 0.25% NA
Temperate Japonica  767 5.50% 94.40% 0.13% 0.00% NA
Tropical Japonica  504 8.70% 91.30% 0.00% 0.00% NA
Japonica Intermediate  241 44.40% 54.80% 0.83% 0.00% NA
VI/Aromatic  96 3.10% 93.80% 3.12% 0.00% NA
Intermediate  90 32.20% 66.70% 1.11% 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
vg1204690369 G -> GCGTACGTTTTCCAAACTGCTAGATGGTGT AATTTTTAGAAAAACTTTATATATGAAAGT TACTTTTAAAAATCACATGTTCTTTCCCCA ACTTTTTCAACTTCTACTTGTTTTTCA LOC_Os12g08960.1 downstream_gene_variant ; 3979.0bp to feature; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> GCGTACGTTTTCCAAACTGCTAGATGGTGT AATTTTTAGAAAAACTTTATATATGAAAGT TACTTTTAAAAATCACATGTTCTTTCCCCA ACTTTTTCAACTTCTACTTGTTTTTCA LOC_Os12g08970.1 downstream_gene_variant ; 4464.0bp to feature; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> GCGTACGTTTTCCAAACTGCTAGATGGTGT AATTTTTAGAAAAACTTTATATATGAAAGT TACTTTTAAAAATCACATGTTCTTTCCCCA ACTTTTTCAACTTCTACTTGTTTTTCA LOC_Os12g08960-LOC_Os12g08970 intergenic_region ; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> DEL N N silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> A LOC_Os12g08960.1 downstream_gene_variant ; 3978.0bp to feature; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> A LOC_Os12g08970.1 downstream_gene_variant ; 4465.0bp to feature; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 N N N N
vg1204690369 G -> A LOC_Os12g08960-LOC_Os12g08970 intergenic_region ; MODIFIER silent_mutation Average:73.088; most accessible tissue: Zhenshan97 panicle, score: 95.264 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)
vg1204690369 G A -0.03 -0.02 -0.02 -0.03 -0.05 -0.04
vg1204690369 G GCGTA* 0.12 -0.33 -0.29 -0.08 -0.2 -0.35

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204690369 NA 2.77E-07 mr1114 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
vg1204690369 NA 7.58E-08 mr1117 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
vg1204690369 NA 1.18E-07 mr1118 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
vg1204690369 NA 6.81E-06 mr1120 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
vg1204690369 7.92E-06 2.67E-09 mr1123 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
vg1204690369 NA 3.59E-06 mr1240 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
vg1204690369 5.83E-06 1.77E-09 mr1242 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
vg1204690369 NA 7.03E-07 mr1247 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
vg1204690369 NA 1.16E-07 mr1496 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
vg1204690369 3.45E-06 NA mr1682 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
vg1204690369 1.52E-06 1.78E-09 mr1691 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
vg1204690369 7.28E-07 1.71E-13 mr1693 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
vg1204690369 NA 2.77E-07 mr1720 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
vg1204690369 NA 5.08E-07 mr1917 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
vg1204690369 NA 8.96E-06 mr1936 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
vg1204690369 NA 5.57E-31 mr1037_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
vg1204690369 NA 3.50E-06 mr1117_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
vg1204690369 NA 9.28E-06 mr1123_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
vg1204690369 NA 2.75E-07 mr1321_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
vg1204690369 NA 1.09E-06 mr1496_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
vg1204690369 NA 4.94E-06 mr1655_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
vg1204690369 5.78E-06 NA mr1679_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
vg1204690369 NA 9.29E-07 mr1679_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
vg1204690369 5.39E-06 5.84E-10 mr1691_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
vg1204690369 NA 4.37E-08 mr1720_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