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Detailed information for vg0526295265:

Variant ID: vg0526295265 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 26295265
Reference Allele: CTAAAlternative Allele: GTAA,C,TTAA
Primary Allele: GTAASecondary Allele: CTAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACCATCGTTGTTCATGATTTCTCCTCTGGAATCGCTGCTGATAGATTGCCGTTGTCGGATCTGGCCTGTTTAGAGCAAGTTTAATAGTATAGCACACTA[CTAA/GTAA,C,TTAA]
CTCTAAATTATCTATAGCCAATGTAATAGCAAATTTGTACAATAGTTACTTACTATACTATTAATACCTGGTCCCACCTGTCATACACGCATTGCTTTTG

Reverse complement sequence

CAAAAGCAATGCGTGTATGACAGGTGGGACCAGGTATTAATAGTATAGTAAGTAACTATTGTACAAATTTGCTATTACATTGGCTATAGATAATTTAGAG[TTAG/TTAC,G,TTAA]
TAGTGTGCTATACTATTAAACTTGCTCTAAACAGGCCAGATCCGACAACGGCAATCTATCAGCAGCGATTCCAGAGGAGAAATCATGAACAACGATGGTC

Allele Frequencies:

Populations Population SizeFrequency of GTAA(primary allele) Frequency of CTAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.70% 38.30% 10.11% 4.63% C: 0.19%; TTAA: 0.04%
All Indica  2759 69.20% 8.80% 14.90% 6.96% C: 0.11%; TTAA: 0.04%
All Japonica  1512 0.90% 98.90% 0.07% 0.07% TTAA: 0.07%
Aus  269 64.70% 2.20% 21.56% 9.29% C: 2.23%
Indica I  595 67.20% 1.20% 25.04% 6.55% NA
Indica II  465 48.80% 31.20% 11.83% 8.17% NA
Indica III  913 82.30% 3.90% 8.00% 5.48% C: 0.22%; TTAA: 0.11%
Indica Intermediate  786 67.70% 6.90% 17.05% 8.27% C: 0.13%
Temperate Japonica  767 1.30% 98.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.00% 0.20% 0.20% TTAA: 0.20%
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 78.10% 18.80% 3.12% 0.00% NA
Intermediate  90 41.10% 52.20% 5.56% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0526295265 CTAA -> DEL N N silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> GTAA LOC_Os05g45310.1 upstream_gene_variant ; 3275.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> GTAA LOC_Os05g45320.1 downstream_gene_variant ; 482.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> GTAA LOC_Os05g45330.1 downstream_gene_variant ; 286.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> GTAA LOC_Os05g45320.2 downstream_gene_variant ; 482.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> GTAA LOC_Os05g45320-LOC_Os05g45330 intergenic_region ; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> C LOC_Os05g45310.1 upstream_gene_variant ; 3276.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> C LOC_Os05g45320.1 downstream_gene_variant ; 483.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> C LOC_Os05g45330.1 downstream_gene_variant ; 285.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> C LOC_Os05g45320.2 downstream_gene_variant ; 483.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> C LOC_Os05g45320-LOC_Os05g45330 intergenic_region ; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> TTAA LOC_Os05g45310.1 upstream_gene_variant ; 3275.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> TTAA LOC_Os05g45320.1 downstream_gene_variant ; 482.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> TTAA LOC_Os05g45330.1 downstream_gene_variant ; 286.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> TTAA LOC_Os05g45320.2 downstream_gene_variant ; 482.0bp to feature; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 N N N N
vg0526295265 CTAA -> TTAA LOC_Os05g45320-LOC_Os05g45330 intergenic_region ; MODIFIER silent_mutation Average:78.401; most accessible tissue: Zhenshan97 panicle, score: 90.467 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)
vg0526295265 CTAA C 0.11 -0.01 -0.05 0.17 0.08 0.02
vg0526295265 CTAA GTAA -0.13 -0.08 -0.05 -0.1 -0.1 -0.08
vg0526295265 CTAA TTAA -0.09 -0.04 -0.02 -0.08 -0.07 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0526295265 NA 1.82E-45 mr1016 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
vg0526295265 NA 7.87E-13 mr1016 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
vg0526295265 NA 2.67E-30 mr1022 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
vg0526295265 NA 4.53E-13 mr1022 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
vg0526295265 NA 6.32E-16 mr1059 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
vg0526295265 NA 6.81E-07 mr1109 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
vg0526295265 NA 1.08E-10 mr1142 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
vg0526295265 NA 6.75E-16 mr1143 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
vg0526295265 NA 4.88E-17 mr1167 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
vg0526295265 NA 1.86E-55 mr1178 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
vg0526295265 NA 3.92E-13 mr1178 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
vg0526295265 NA 1.10E-13 mr1478 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
vg0526295265 NA 5.19E-06 mr1478 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
vg0526295265 NA 2.01E-11 mr1490 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
vg0526295265 NA 8.71E-16 mr1535 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
vg0526295265 NA 9.52E-07 mr1599 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
vg0526295265 NA 1.29E-10 mr1623 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
vg0526295265 NA 2.69E-16 mr1675 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
vg0526295265 NA 1.84E-06 mr1677 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
vg0526295265 NA 9.60E-40 mr1719 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
vg0526295265 2.75E-09 1.90E-08 mr1719 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
vg0526295265 NA 3.40E-14 mr1726 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
vg0526295265 NA 2.45E-25 mr1903 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
vg0526295265 NA 1.03E-11 mr1938 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
vg0526295265 NA 4.33E-15 mr1950 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
vg0526295265 NA 7.28E-16 mr1969 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
vg0526295265 NA 1.51E-17 mr1995 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
vg0526295265 NA 1.33E-08 mr1030_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
vg0526295265 NA 2.74E-08 mr1089_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
vg0526295265 NA 2.72E-09 mr1093_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
vg0526295265 NA 2.91E-10 mr1109_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
vg0526295265 NA 4.62E-55 mr1141_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
vg0526295265 NA 7.98E-06 mr1193_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
vg0526295265 NA 1.52E-22 mr1195_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
vg0526295265 NA 2.32E-11 mr1195_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
vg0526295265 NA 9.18E-10 mr1235_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
vg0526295265 NA 9.50E-40 mr1243_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
vg0526295265 NA 3.57E-07 mr1243_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
vg0526295265 NA 9.78E-21 mr1253_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
vg0526295265 NA 1.21E-06 mr1253_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
vg0526295265 NA 2.23E-10 mr1352_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
vg0526295265 NA 3.18E-07 mr1358_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
vg0526295265 NA 3.55E-07 mr1408_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
vg0526295265 NA 5.10E-06 mr1423_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
vg0526295265 NA 7.45E-09 mr1478_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
vg0526295265 NA 1.06E-52 mr1546_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
vg0526295265 NA 8.16E-13 mr1546_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
vg0526295265 NA 3.84E-06 mr1555_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
vg0526295265 NA 2.20E-16 mr1587_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
vg0526295265 NA 3.51E-61 mr1599_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
vg0526295265 NA 3.78E-11 mr1599_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
vg0526295265 NA 1.53E-06 mr1682_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
vg0526295265 NA 4.04E-07 mr1805_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
vg0526295265 NA 1.61E-07 mr1821_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
vg0526295265 6.37E-08 1.04E-75 mr1828_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
vg0526295265 1.33E-06 1.34E-11 mr1828_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
vg0526295265 NA 2.02E-07 mr1837_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
vg0526295265 NA 4.49E-11 mr1893_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
vg0526295265 NA 2.64E-06 mr1915_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
vg0526295265 NA 1.15E-15 mr1938_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
vg0526295265 NA 9.31E-07 mr1938_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