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Detailed information for vg1002821112:

Variant ID: vg1002821112 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 2821112
Reference Allele: TAAlternative Allele: TAA,CA,T,AA
Primary Allele: TASecondary Allele: CA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCTCGAACTATACAAACCGGACGAATTACCCCCCTTATCCAATCCGCAGTGGTTTTGGTCTACGTGGCGTACGCGTGGCAGTCCAGTCAGCGTTCTATA[TA/TAA,CA,T,AA]
AAAAAAATGTGGGGCCTACATGTCATACACTCTTCTCTCTCTTCTCTCTCACTCTCCTCACTCTTCTCATTCTTCCCCTCTCTCTCTCACGGTCAGCGGC

Reverse complement sequence

GCCGCTGACCGTGAGAGAGAGAGGGGAAGAATGAGAAGAGTGAGGAGAGTGAGAGAGAAGAGAGAGAAGAGTGTATGACATGTAGGCCCCACATTTTTTT[TA/TTA,TG,A,TT]
TATAGAACGCTGACTGGACTGCCACGCGTACGCCACGTAGACCAAAACCACTGCGGATTGGATAAGGGGGGTAATTCGTCCGGTTTGTATAGTTCGAGGT

Allele Frequencies:

Populations Population SizeFrequency of TA(primary allele) Frequency of CA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.60% 17.10% 0.93% 0.00% TAA: 7.62%; T: 0.68%; AA: 0.13%
All Indica  2759 87.60% 3.40% 0.29% 0.00% TAA: 8.26%; T: 0.51%
All Japonica  1512 58.10% 38.10% 1.92% 0.00% TAA: 0.73%; T: 0.73%; AA: 0.40%
Aus  269 14.10% 45.70% 1.12% 0.00% TAA: 37.55%; T: 1.49%
Indica I  595 97.30% 0.00% 0.50% 0.00% TAA: 2.02%; T: 0.17%
Indica II  465 69.90% 0.60% 0.00% 0.00% TAA: 29.03%; T: 0.43%
Indica III  913 91.00% 6.10% 0.44% 0.00% TAA: 1.64%; T: 0.77%
Indica Intermediate  786 86.60% 4.30% 0.13% 0.00% TAA: 8.40%; T: 0.51%
Temperate Japonica  767 87.10% 11.70% 0.65% 0.00% TAA: 0.26%; T: 0.26%
Tropical Japonica  504 12.50% 81.50% 3.17% 0.00% T: 1.39%; AA: 1.19%; TAA: 0.20%
Japonica Intermediate  241 61.40% 31.10% 3.32% 0.00% TAA: 3.32%; T: 0.83%
VI/Aromatic  96 92.70% 1.00% 1.04% 0.00% TAA: 4.17%; T: 1.04%
Intermediate  90 60.00% 16.70% 3.33% 0.00% TAA: 17.78%; T: 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
vg1002821112 TA -> TAA LOC_Os10g05650.1 upstream_gene_variant ; 1491.0bp to feature; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> TAA LOC_Os10g05650-LOC_Os10g05660 intergenic_region ; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> CA LOC_Os10g05650.1 upstream_gene_variant ; 1489.0bp to feature; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> CA LOC_Os10g05650-LOC_Os10g05660 intergenic_region ; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> AA LOC_Os10g05650.1 upstream_gene_variant ; 1489.0bp to feature; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> AA LOC_Os10g05650-LOC_Os10g05660 intergenic_region ; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> T LOC_Os10g05650.1 upstream_gene_variant ; 1490.0bp to feature; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 N N N N
vg1002821112 TA -> T LOC_Os10g05650-LOC_Os10g05660 intergenic_region ; MODIFIER silent_mutation Average:73.097; most accessible tissue: Minghui63 root, score: 90.465 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)
vg1002821112 TA AA -0.01 -0.01 -0.01 -0.02 -0.01 -0.01
vg1002821112 TA CA -0.04 -0.02 0.0 -0.01 0.0 0.0
vg1002821112 TA T -0.02 -0.03 0.0 -0.02 -0.02 -0.04
vg1002821112 TA TAA -0.01 0.01 0.01 -0.06 -0.05 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002821112 NA 1.31E-08 mr1118 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
vg1002821112 NA 2.44E-07 mr1123 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
vg1002821112 2.67E-06 2.67E-06 mr1146 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
vg1002821112 NA 1.47E-06 mr1179 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
vg1002821112 NA 3.30E-07 mr1220 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
vg1002821112 NA 4.94E-06 mr1220 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
vg1002821112 NA 7.36E-06 mr1242 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
vg1002821112 5.51E-06 1.50E-11 mr1248 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
vg1002821112 NA 2.80E-09 mr1248 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
vg1002821112 NA 1.38E-07 mr1338 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
vg1002821112 NA 9.92E-06 mr1378 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
vg1002821112 NA 1.74E-06 mr1425 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
vg1002821112 NA 1.32E-09 mr1495 Jap_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
vg1002821112 NA 2.24E-06 mr1527 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
vg1002821112 NA 2.37E-10 mr1539 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
vg1002821112 NA 1.17E-10 mr1580 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
vg1002821112 NA 2.30E-06 mr1603 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
vg1002821112 NA 7.35E-06 mr1642 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
vg1002821112 NA 2.67E-10 mr1679 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
vg1002821112 NA 2.56E-07 mr1693 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
vg1002821112 NA 1.18E-15 mr1699 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
vg1002821112 NA 7.81E-06 mr1720 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
vg1002821112 6.10E-06 1.94E-09 mr1736 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
vg1002821112 NA 4.06E-06 mr1768 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
vg1002821112 NA 1.38E-18 mr1825 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
vg1002821112 NA 1.00E-09 mr1825 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
vg1002821112 NA 4.45E-06 mr1858 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
vg1002821112 NA 4.47E-06 mr1859 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
vg1002821112 NA 1.57E-06 mr1870 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
vg1002821112 NA 8.71E-06 mr1912 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
vg1002821112 NA 4.44E-07 mr1936 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
vg1002821112 NA 2.07E-07 mr1951 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
vg1002821112 NA 2.74E-07 mr1118_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
vg1002821112 NA 3.52E-08 mr1495_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
vg1002821112 NA 2.18E-07 mr1679_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
vg1002821112 NA 8.65E-06 mr1936_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