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Detailed information for vg0129164753:

Variant ID: vg0129164753 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 29164753
Reference Allele: AAlternative Allele: T,ATTT,ATTTT
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTTTCCGCATGGACGTTTTTCAAACTGCTAAACGGTGTGTTTTTTGCAAAAAAAAACTATACGAAAGTTGTTTTAAAAATCAAATTAATCTATTTTTTA[A/T,ATTT,ATTTT]
AAAAATAGTTAATACTTAATTAATCATCCAATAATACGTATTTTGTTGTGCGTGCCGGGGAGGAGCTCCCGAAGACAGCCTTAGACTTCATCATCTCCAA

Reverse complement sequence

TTGGAGATGATGAAGTCTAAGGCTGTCTTCGGGAGCTCCTCCCCGGCACGCACAACAAAATACGTATTATTGGATGATTAATTAAGTATTAACTATTTTT[T/A,AAAT,AAAAT]
TAAAAAATAGATTAATTTGATTTTTAAAACAACTTTCGTATAGTTTTTTTTTGCAAAAAACACACCGTTTAGCAGTTTGAAAAACGTCCATGCGGAAAAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.00% 45.00% 0.25% 0.00% ATTT: 4.72%; ATTTT: 0.02%
All Indica  2759 76.40% 15.40% 0.22% 0.00% ATTT: 7.94%; ATTTT: 0.04%
All Japonica  1512 9.30% 90.30% 0.40% 0.00% NA
Aus  269 4.80% 95.20% 0.00% 0.00% NA
Indica I  595 57.60% 38.50% 0.34% 0.00% ATTT: 3.53%
Indica II  465 97.00% 2.80% 0.00% 0.00% ATTT: 0.22%
Indica III  913 76.70% 7.60% 0.22% 0.00% ATTT: 15.44%; ATTTT: 0.11%
Indica Intermediate  786 78.10% 14.50% 0.25% 0.00% ATTT: 7.12%
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 26.40% 73.00% 0.60% 0.00% NA
Japonica Intermediate  241 2.90% 95.90% 1.24% 0.00% NA
VI/Aromatic  96 63.50% 35.40% 0.00% 0.00% ATTT: 1.04%
Intermediate  90 42.20% 54.40% 0.00% 0.00% ATTT: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0129164753 A -> T LOC_Os01g50770.1 upstream_gene_variant ; 1666.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> T LOC_Os01g50770.2 upstream_gene_variant ; 1666.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> T LOC_Os01g50760.1 downstream_gene_variant ; 2035.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> T LOC_Os01g50760-LOC_Os01g50770 intergenic_region ; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTTT LOC_Os01g50770.1 upstream_gene_variant ; 1665.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTTT LOC_Os01g50770.2 upstream_gene_variant ; 1665.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTTT LOC_Os01g50760.1 downstream_gene_variant ; 2036.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTTT LOC_Os01g50760-LOC_Os01g50770 intergenic_region ; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTT LOC_Os01g50770.1 upstream_gene_variant ; 1665.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTT LOC_Os01g50770.2 upstream_gene_variant ; 1665.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTT LOC_Os01g50760.1 downstream_gene_variant ; 2036.0bp to feature; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 N N N N
vg0129164753 A -> ATTT LOC_Os01g50760-LOC_Os01g50770 intergenic_region ; MODIFIER silent_mutation Average:49.997; most accessible tissue: Zhenshan97 flag leaf, score: 85.638 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)
vg0129164753 A ATTT -0.08 -0.22 -0.18 -0.05 -0.02 -0.03
vg0129164753 A ATTTT -0.01 -0.1 -0.08 -0.05 0.0 -0.01
vg0129164753 A T -0.01 0.0 -0.01 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129164753 NA 1.29E-19 Plant_height Ind_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
vg0129164753 NA 1.99E-08 mr1011 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
vg0129164753 NA 3.90E-07 mr1011 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
vg0129164753 NA 7.40E-06 mr1012 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
vg0129164753 NA 5.39E-17 mr1013 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
vg0129164753 NA 5.00E-08 mr1013 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
vg0129164753 NA 3.16E-06 mr1014 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
vg0129164753 NA 2.80E-06 mr1021 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
vg0129164753 NA 5.22E-18 mr1031 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
vg0129164753 NA 3.78E-10 mr1031 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
vg0129164753 NA 1.23E-07 mr1032 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
vg0129164753 NA 1.33E-15 mr1034 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
vg0129164753 NA 5.92E-07 mr1034 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
vg0129164753 NA 9.54E-18 mr1056 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
vg0129164753 NA 1.52E-09 mr1056 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
vg0129164753 NA 9.54E-08 mr1157 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
vg0129164753 NA 7.11E-06 mr1165 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
vg0129164753 NA 3.57E-18 mr1255 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
vg0129164753 NA 1.41E-06 mr1477 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
vg0129164753 NA 8.56E-07 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
vg0129164753 NA 3.99E-06 mr1502 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
vg0129164753 NA 2.12E-06 mr1692 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
vg0129164753 NA 2.04E-06 mr1706 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
vg0129164753 NA 2.67E-07 mr1717 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
vg0129164753 NA 1.34E-15 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
vg0129164753 NA 7.29E-09 mr1839 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
vg0129164753 NA 3.68E-06 mr1909 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
vg0129164753 NA 2.46E-06 mr1971 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
vg0129164753 NA 1.20E-10 mr1011_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
vg0129164753 NA 2.37E-06 mr1013_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
vg0129164753 NA 3.66E-06 mr1015_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
vg0129164753 NA 2.93E-07 mr1031_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
vg0129164753 NA 3.80E-09 mr1060_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
vg0129164753 NA 1.94E-08 mr1064_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
vg0129164753 NA 1.33E-06 mr1115_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
vg0129164753 NA 7.54E-06 mr1128_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
vg0129164753 NA 3.50E-06 mr1165_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
vg0129164753 NA 1.58E-08 mr1172_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
vg0129164753 NA 1.45E-09 mr1174_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
vg0129164753 NA 1.85E-21 mr1183_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
vg0129164753 NA 5.39E-06 mr1268_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
vg0129164753 NA 7.80E-10 mr1268_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
vg0129164753 NA 1.65E-06 mr1274_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
vg0129164753 NA 1.79E-08 mr1327_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
vg0129164753 NA 1.21E-08 mr1327_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
vg0129164753 NA 2.66E-17 mr1352_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
vg0129164753 NA 1.22E-09 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
vg0129164753 NA 5.25E-06 mr1358_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
vg0129164753 NA 2.27E-06 mr1359_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
vg0129164753 NA 4.66E-09 mr1478_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
vg0129164753 NA 1.99E-06 mr1480_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
vg0129164753 NA 2.37E-07 mr1611_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
vg0129164753 NA 8.34E-06 mr1624_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
vg0129164753 NA 8.83E-09 mr1627_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
vg0129164753 NA 1.81E-07 mr1636_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
vg0129164753 NA 8.73E-07 mr1641_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
vg0129164753 NA 3.27E-08 mr1653_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
vg0129164753 NA 5.03E-06 mr1671_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
vg0129164753 NA 4.67E-07 mr1735_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
vg0129164753 NA 3.05E-09 mr1758_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
vg0129164753 NA 1.53E-16 mr1807_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
vg0129164753 NA 1.47E-06 mr1820_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
vg0129164753 NA 1.96E-06 mr1836_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
vg0129164753 NA 3.12E-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
vg0129164753 NA 4.35E-07 mr1838_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
vg0129164753 NA 9.51E-06 mr1959_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
vg0129164753 NA 7.11E-07 mr1971_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