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Detailed information for vg0604730580:

Variant ID: vg0604730580 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 4730580
Reference Allele: CAlternative Allele: T,CAAGACT
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTGAAGCCAGCAGTTGGCTATACTATTAAACTTGCTCTTAGACGACAAAAAGCCTAAAATGACTGGTGGAATCTTCTTTTGAGACCATATATACAC[C/T,CAAGACT]
CAAGGGACAAAAATAGTAAGACAATCTAGAGAACATTTTAATACGATTGTTGCCGTGACTTTGTAACCCCAAGTTTAGTGTTTTAGTTGCCTTTATCAAT

Reverse complement sequence

ATTGATAAAGGCAACTAAAACACTAAACTTGGGGTTACAAAGTCACGGCAACAATCGTATTAAAATGTTCTCTAGATTGTCTTACTATTTTTGTCCCTTG[G/A,AGTCTTG]
GTGTATATATGGTCTCAAAAGAAGATTCCACCAGTCATTTTAGGCTTTTTGTCGTCTAAGAGCAAGTTTAATAGTATAGCCAACTGCTGGCTTCAAATCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.80% 16.10% 0.04% 0.00% CAAGACT: 0.02%
All Indica  2759 99.20% 0.80% 0.04% 0.00% NA
All Japonica  1512 51.20% 48.70% 0.07% 0.00% CAAGACT: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 21.60% 78.40% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 7.50% 0.00% 0.00% CAAGACT: 0.20%
Japonica Intermediate  241 59.30% 40.20% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 0.00% 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
vg0604730580 C -> CAAGACT LOC_Os06g09390.1 upstream_gene_variant ; 749.0bp to feature; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 N N N N
vg0604730580 C -> CAAGACT LOC_Os06g09390.2 upstream_gene_variant ; 749.0bp to feature; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 N N N N
vg0604730580 C -> CAAGACT LOC_Os06g09380-LOC_Os06g09390 intergenic_region ; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 N N N N
vg0604730580 C -> T LOC_Os06g09390.1 upstream_gene_variant ; 750.0bp to feature; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 N N N N
vg0604730580 C -> T LOC_Os06g09390.2 upstream_gene_variant ; 750.0bp to feature; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 N N N N
vg0604730580 C -> T LOC_Os06g09380-LOC_Os06g09390 intergenic_region ; MODIFIER silent_mutation Average:81.006; most accessible tissue: Zhenshan97 flower, score: 96.696 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)
vg0604730580 C CAAGA* 0.46 -0.11 -0.19 -0.02 0.05 -0.1
vg0604730580 C T -0.05 -0.07 -0.07 -0.02 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604730580 NA 1.11E-13 Spikelet_length 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
vg0604730580 NA 9.69E-06 mr1006 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
vg0604730580 2.77E-06 NA mr1050 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
vg0604730580 7.98E-06 2.36E-07 mr1050 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
vg0604730580 NA 3.43E-06 mr1063 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
vg0604730580 9.69E-09 6.33E-30 mr1115 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
vg0604730580 2.14E-06 7.10E-19 mr1115 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
vg0604730580 9.06E-07 5.06E-37 mr1137 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
vg0604730580 NA 2.22E-11 mr1137 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
vg0604730580 NA 3.82E-06 mr1263 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
vg0604730580 NA 3.94E-06 mr1272 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
vg0604730580 NA 1.82E-06 mr1280 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
vg0604730580 NA 8.54E-06 mr1318 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
vg0604730580 NA 3.82E-06 mr1451 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
vg0604730580 NA 1.72E-06 mr1521 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
vg0604730580 NA 7.34E-08 mr1531 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
vg0604730580 NA 6.64E-06 mr1576 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
vg0604730580 7.69E-08 3.34E-29 mr1611 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
vg0604730580 1.64E-06 8.26E-17 mr1611 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
vg0604730580 1.72E-06 3.44E-31 mr1617 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
vg0604730580 NA 1.23E-09 mr1617 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
vg0604730580 NA 2.32E-06 mr1729 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
vg0604730580 NA 1.19E-06 mr1788 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
vg0604730580 3.57E-10 1.09E-30 mr1920 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
vg0604730580 1.30E-07 1.68E-16 mr1920 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
vg0604730580 NA 6.42E-29 mr1115_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
vg0604730580 NA 2.44E-15 mr1115_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
vg0604730580 7.29E-08 4.86E-42 mr1137_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
vg0604730580 NA 1.88E-11 mr1137_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
vg0604730580 NA 1.47E-27 mr1611_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
vg0604730580 NA 1.30E-14 mr1611_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
vg0604730580 4.66E-06 2.82E-30 mr1617_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
vg0604730580 NA 2.24E-08 mr1617_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
vg0604730580 NA 1.01E-08 mr1741_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