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Detailed information for vg0523014690:

Variant ID: vg0523014690 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 23014690
Reference Allele: TTCAlternative Allele: CTC,T
Primary Allele: TTCSecondary Allele: CTC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTTACCTGTTTAGAAGGATGAGGTTATTACCTGTTTTGTTTGGTTGGGAGACATGAAAATTTTGATGGGATGGAGATGGGGAATTGAGGAAGGAACTCT[TTC/CTC,T]
CTTTTCAATACCTTGGTAGGGGTGGTAATTTGGAGGGAATTCCTCATTTACTTTACCTAAACAAATCTCAGCTAACCGTTTTCATTAATGACCTAATCTC

Reverse complement sequence

GAGATTAGGTCATTAATGAAAACGGTTAGCTGAGATTTGTTTAGGTAAAGTAAATGAGGAATTCCCTCCAAATTACCACCCCTACCAAGGTATTGAAAAG[GAA/GAG,A]
AGAGTTCCTTCCTCAATTCCCCATCTCCATCCCATCAAAATTTTCATGTCTCCCAACCAAACAAAACAGGTAATAACCTCATCCTTCTAAACAGGTAAAA

Allele Frequencies:

Populations Population SizeFrequency of TTC(primary allele) Frequency of CTC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.20% 32.00% 6.88% 26.87% T: 0.02%
All Indica  2759 1.20% 46.10% 10.69% 42.04% T: 0.04%
All Japonica  1512 98.70% 0.80% 0.20% 0.26% NA
Aus  269 1.10% 63.60% 7.81% 27.51% NA
Indica I  595 0.80% 31.60% 22.52% 45.04% NA
Indica II  465 1.50% 41.70% 10.54% 46.24% NA
Indica III  913 0.50% 60.20% 3.83% 35.27% T: 0.11%
Indica Intermediate  786 1.90% 43.10% 9.80% 45.17% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 98.00% 1.00% 0.40% 0.60% NA
Japonica Intermediate  241 97.90% 1.20% 0.41% 0.41% NA
VI/Aromatic  96 56.20% 40.60% 1.04% 2.08% NA
Intermediate  90 37.80% 23.30% 5.56% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0523014690 TTC -> T LOC_Os05g39250.1 upstream_gene_variant ; 337.0bp to feature; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> T LOC_Os05g39240.1 downstream_gene_variant ; 1258.0bp to feature; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> T LOC_Os05g39250-LOC_Os05g39260 intergenic_region ; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> DEL N N silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> CTC LOC_Os05g39250.1 upstream_gene_variant ; 336.0bp to feature; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> CTC LOC_Os05g39240.1 downstream_gene_variant ; 1257.0bp to feature; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 N N N N
vg0523014690 TTC -> CTC LOC_Os05g39250-LOC_Os05g39260 intergenic_region ; MODIFIER silent_mutation Average:91.708; most accessible tissue: Minghui63 panicle, score: 98.35 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)
vg0523014690 TTC CTC 0.0 -0.01 -0.02 0.0 0.0 -0.01
vg0523014690 TTC T 0.05 -0.01 -0.1 -0.04 -0.03 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0523014690 NA 1.72E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0523014690 NA 9.28E-22 mr1122 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
vg0523014690 NA 3.58E-43 mr1194 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
vg0523014690 NA 1.80E-43 mr1480 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
vg0523014690 NA 3.06E-09 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
vg0523014690 NA 1.40E-51 mr1692 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
vg0523014690 NA 8.13E-20 mr1715 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
vg0523014690 NA 3.80E-16 mr1968 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
vg0523014690 NA 2.60E-32 mr1102_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
vg0523014690 NA 4.62E-34 mr1105_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
vg0523014690 NA 2.77E-06 mr1153_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
vg0523014690 NA 7.04E-14 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
vg0523014690 NA 7.26E-54 mr1194_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
vg0523014690 NA 2.87E-09 mr1198_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
vg0523014690 NA 2.04E-35 mr1223_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
vg0523014690 NA 1.68E-09 mr1232_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
vg0523014690 NA 1.71E-12 mr1258_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
vg0523014690 NA 7.52E-08 mr1275_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
vg0523014690 NA 9.84E-23 mr1298_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
vg0523014690 NA 5.09E-57 mr1480_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
vg0523014690 NA 1.93E-09 mr1506_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
vg0523014690 NA 5.57E-15 mr1529_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
vg0523014690 NA 3.35E-17 mr1557_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
vg0523014690 NA 7.06E-06 mr1574_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
vg0523014690 NA 3.57E-12 mr1641_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
vg0523014690 NA 4.53E-08 mr1659_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
vg0523014690 NA 4.59E-08 mr1681_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
vg0523014690 NA 3.68E-83 mr1711_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
vg0523014690 NA 7.15E-12 mr1714_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
vg0523014690 NA 6.99E-15 mr1726_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
vg0523014690 NA 9.82E-17 mr1730_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
vg0523014690 NA 1.56E-21 mr1731_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
vg0523014690 NA 4.98E-17 mr1767_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
vg0523014690 NA 4.03E-11 mr1806_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
vg0523014690 NA 1.82E-13 mr1838_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
vg0523014690 NA 5.59E-16 mr1866_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
vg0523014690 NA 4.46E-34 mr1873_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
vg0523014690 NA 4.64E-67 mr1896_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
vg0523014690 NA 6.77E-94 mr1907_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
vg0523014690 NA 2.38E-08 mr1909_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
vg0523014690 NA 5.49E-08 mr1921_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
vg0523014690 NA 1.81E-19 mr1922_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
vg0523014690 NA 2.76E-90 mr1934_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
vg0523014690 NA 7.18E-15 mr1950_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
vg0523014690 NA 3.50E-22 mr1968_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
vg0523014690 NA 2.25E-14 mr1986_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