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Detailed information for vg1126584071:

Variant ID: vg1126584071 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 26584071
Reference Allele: GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTAAlternative Allele: AGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA,G,TGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA
Primary Allele: GGGCCTCTTCGCCCTCGCCG TCGACTTCTCCTASecondary Allele: AGGCCTCTTCGCCCTCGCCG TCGACTTCTCCTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTCTCCGCCGGCGGCGAGCCGCTGCTCCTCGTGTGGAGGCTCTCCCTCCTCCTCACCGCCTACTTCTTCCTCTGCGCCGCCCTCCTCTCCCTCACCAC[GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA/AGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA,G,TGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA]
CGGCGCCTTGCTGGCCTACTTCGCCGGCCATGCCATCACCCCGCGCGTCGGGATGGTTGTAGTCTTCCTCAACTCCGTCTCCGCCGCGGCCATGGCGGGC

Reverse complement sequence

GCCCGCCATGGCCGCGGCGGAGACGGAGTTGAGGAAGACTACAACCATCCCGACGCGCGGGGTGATGGCATGGCCGGCGAAGTAGGCCAGCAAGGCGCCG[TAGGAGAAGTCGACGGCGAGGGCGAAGAGGCCC/TAGGAGAAGTCGACGGCGAGGGCGAAGAGGCCT,C,TAGGAGAAGTCGACGGCGAGGGCGAAGAGGCCA]
GTGGTGAGGGAGAGGAGGGCGGCGCAGAGGAAGAAGTAGGCGGTGAGGAGGAGGGAGAGCCTCCACACGAGGAGCAGCGGCTCGCCGCCGGCGGAGAGCC

Allele Frequencies:

Populations Population SizeFrequency of GGGCCTCTTCGCCCTCGCCG TCGACTTCTCCTA(primary allele) Frequency of AGGCCTCTTCGCCCTCGCCG TCGACTTCTCCTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.60% 7.10% 0.99% 4.08% G: 0.19%; TGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA: 0.02%
All Indica  2759 81.10% 10.80% 1.59% 6.13% G: 0.33%; TGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA: 0.04%
All Japonica  1512 99.30% 0.40% 0.00% 0.33% NA
Aus  269 87.70% 7.10% 0.00% 5.20% NA
Indica I  595 69.20% 12.80% 3.70% 14.29% NA
Indica II  465 82.60% 7.30% 2.15% 7.96% NA
Indica III  913 84.20% 12.70% 0.88% 1.20% G: 0.99%
Indica Intermediate  786 85.50% 9.30% 0.51% 4.58% TGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA: 0.13%
Temperate Japonica  767 98.70% 0.70% 0.00% 0.65% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 12.20% 3.33% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126584071 GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA -> TGGCCTCTTCGCCCTCGCCGTCGACTTCTC CTA LOC_Os11g44000.1 synonymous_variant ; p.Thr113Thr; LOW synonymous_codon Average:81.004; most accessible tissue: Zhenshan97 panicle, score: 94.518 N N N N
vg1126584071 GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA -> AGGCCTCTTCGCCCTCGCCGTCGACTTCTC CTA LOC_Os11g44000.1 synonymous_variant ; p.Thr113Thr; LOW synonymous_codon Average:81.004; most accessible tissue: Zhenshan97 panicle, score: 94.518 N N N N
vg1126584071 GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA -> DEL LOC_Os11g44000.1 N frameshift_variant Average:81.004; most accessible tissue: Zhenshan97 panicle, score: 94.518 N N N N
vg1126584071 GGGCCTCTTCGCCCTCGCCGTCGACTTCTCCTA -> G LOC_Os11g44000.1 frameshift_variant ; p.Gly114fs; HIGH frameshift_variant Average:81.004; most accessible tissue: Zhenshan97 panicle, score: 94.518 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)
vg1126584071 GGGCC* AGGCC* 0.0 0.01 0.0 0.0 0.0 0.0
vg1126584071 GGGCC* G 0.33 0.33 0.46 0.2 0.41 0.4
vg1126584071 GGGCC* TGGCC* -0.05 -0.01 -0.04 -0.02 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126584071 NA 1.91E-13 mr1191 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
vg1126584071 NA 1.51E-09 mr1191 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
vg1126584071 NA 1.74E-06 mr1295 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
vg1126584071 NA 1.12E-06 mr1295 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
vg1126584071 4.91E-06 1.00E-08 mr1561 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
vg1126584071 NA 9.78E-06 mr1588 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
vg1126584071 NA 6.65E-14 mr1644 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
vg1126584071 NA 3.36E-10 mr1644 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
vg1126584071 7.23E-07 1.72E-08 mr1662 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
vg1126584071 9.54E-06 1.72E-07 mr1662 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
vg1126584071 4.80E-06 9.24E-08 mr1908 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
vg1126584071 1.06E-07 1.11E-20 mr1191_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
vg1126584071 1.00E-07 1.31E-14 mr1191_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
vg1126584071 1.91E-08 7.63E-10 mr1380_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
vg1126584071 7.63E-09 6.75E-09 mr1380_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
vg1126584071 8.27E-09 5.23E-11 mr1561_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
vg1126584071 1.32E-08 6.77E-09 mr1561_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
vg1126584071 NA 3.26E-08 mr1662_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
vg1126584071 NA 3.46E-07 mr1662_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
vg1126584071 NA 7.29E-06 mr1745_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
vg1126584071 4.25E-09 2.61E-12 mr1875_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
vg1126584071 1.79E-08 1.18E-08 mr1875_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
vg1126584071 1.94E-09 1.18E-12 mr1908_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
vg1126584071 3.61E-08 8.23E-09 mr1908_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
vg1126584071 9.58E-08 2.95E-08 mr1996_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
vg1126584071 4.16E-07 7.65E-07 mr1996_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