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Detailed information for vg0500588944:

Variant ID: vg0500588944 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 588944
Reference Allele: CAlternative Allele: T,CAATAA
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCGATCAACGTTTGACCATTCGTTTTATTCAGAAATTTTGTGCAAATATAAAAATATTTATGTTCAACTTAAAGAACATTTGATGACGAATCAAGTCA[C/T,CAATAA]
AATAAAATAAATGATAGTTACATAAATTTTTTGAACAAGACGAATGGTCAAATATTAGACAAAAAATTAACGACGTCATACATTAAAATATGGAGGTAGT

Reverse complement sequence

ACTACCTCCATATTTTAATGTATGACGTCGTTAATTTTTTGTCTAATATTTGACCATTCGTCTTGTTCAAAAAATTTATGTAACTATCATTTATTTTATT[G/A,TTATTG]
TGACTTGATTCGTCATCAAATGTTCTTTAAGTTGAACATAAATATTTTTATATTTGCACAAAATTTCTGAATAAAACGAATGGTCAAACGTTGATCGAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.00% 37.20% 0.47% 0.21% CAATAA: 3.05%
All Indica  2759 35.70% 59.90% 0.65% 0.36% CAATAA: 3.37%
All Japonica  1512 95.90% 3.80% 0.00% 0.00% CAATAA: 0.33%
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 3.00% 94.30% 0.67% 1.18% CAATAA: 0.84%
Indica II  465 48.40% 50.50% 0.65% 0.00% CAATAA: 0.43%
Indica III  913 49.40% 41.80% 0.55% 0.11% CAATAA: 8.11%
Indica Intermediate  786 37.20% 60.30% 0.76% 0.25% CAATAA: 1.53%
Temperate Japonica  767 93.20% 6.60% 0.00% 0.00% CAATAA: 0.13%
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 2.50% 0.00% 0.00% CAATAA: 1.66%
VI/Aromatic  96 41.70% 12.50% 0.00% 0.00% CAATAA: 45.83%
Intermediate  90 66.70% 26.70% 4.44% 0.00% CAATAA: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0500588944 C -> T LOC_Os05g02030.1 upstream_gene_variant ; 1322.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> T LOC_Os05g02040.1 upstream_gene_variant ; 4412.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> T LOC_Os05g02020-LOC_Os05g02030 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> CAATAA LOC_Os05g02030.1 upstream_gene_variant ; 1321.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> CAATAA LOC_Os05g02040.1 upstream_gene_variant ; 4411.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> CAATAA LOC_Os05g02020-LOC_Os05g02030 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500588944 C -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0500588944 C CAATA* 0.48 0.14 0.1 0.06 0.24 0.34
vg0500588944 C T -0.02 -0.01 -0.02 0.02 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500588944 NA 8.22E-06 mr1074 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
vg0500588944 NA 5.00E-07 mr1130 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
vg0500588944 NA 1.60E-06 mr1215 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
vg0500588944 NA 9.44E-06 mr1318 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
vg0500588944 1.18E-06 1.18E-06 mr1440 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
vg0500588944 NA 9.04E-06 mr1511 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
vg0500588944 NA 4.15E-16 mr1531 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
vg0500588944 NA 9.44E-06 mr1607 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
vg0500588944 NA 2.62E-06 mr1669 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
vg0500588944 NA 3.72E-08 mr1707 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
vg0500588944 NA 4.59E-08 mr1728 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
vg0500588944 NA 6.83E-06 mr1741 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
vg0500588944 NA 9.42E-11 mr1751 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
vg0500588944 NA 2.49E-18 mr1807 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
vg0500588944 NA 6.43E-06 mr1807 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
vg0500588944 NA 7.19E-07 mr1958 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
vg0500588944 NA 1.68E-08 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
vg0500588944 NA 6.29E-06 mr1322_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
vg0500588944 NA 3.02E-06 mr1875_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
vg0500588944 NA 5.85E-06 mr1899_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
vg0500588944 NA 1.00E-07 mr1910_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
vg0500588944 NA 1.27E-11 mr1946_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
vg0500588944 NA 1.27E-11 mr1948_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