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Detailed information for vg0807357132:

Variant ID: vg0807357132 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 7357132
Reference Allele: TAlternative Allele: C,TCCCGCGTCGTTGTTTCACGGCAC
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGCGGTAGCGTGGTAGTGAGCAGGACCGTGCCGCATCAAAACGGTCCCGCGGCATGAAAGAACGGAACCAATATGGTCCCGCGTAGCCATTGCACAGCA[T/C,TCCCGCGTCGTTGTTTCACGGCAC]
CGAGGTGGTCCCGCGTCGTTGTTTCACGGCACCGAGGTGGTCCCGCGTCGGTGTTTCACGGCACCGCGTCGGTCTCGAGGATGACGGAGACAACAAGACT

Reverse complement sequence

AGTCTTGTTGTCTCCGTCATCCTCGAGACCGACGCGGTGCCGTGAAACACCGACGCGGGACCACCTCGGTGCCGTGAAACAACGACGCGGGACCACCTCG[A/G,GTGCCGTGAAACAACGACGCGGGA]
TGCTGTGCAATGGCTACGCGGGACCATATTGGTTCCGTTCTTTCATGCCGCGGGACCGTTTTGATGCGGCACGGTCCTGCTCACTACCACGCTACCGCTC

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 63.50% 36.20% 0.32% 0.00% TCCCGCGTCGTTGTTTCACGGCAC: 0.02%
All Indica  2759 92.00% 7.80% 0.14% 0.00% TCCCGCGTCGTTGTTTCACGGCAC: 0.04%
All Japonica  1512 3.20% 96.10% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.60% 2.20% 0.17% 0.00% NA
Indica II  465 97.00% 2.80% 0.22% 0.00% NA
Indica III  913 88.10% 11.70% 0.22% 0.00% NA
Indica Intermediate  786 89.30% 10.60% 0.00% 0.00% TCCCGCGTCGTTGTTTCACGGCAC: 0.13%
Temperate Japonica  767 2.50% 96.60% 0.91% 0.00% NA
Tropical Japonica  504 4.00% 96.00% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 94.60% 1.24% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 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
vg0807357132 T -> C LOC_Os08g12440.1 upstream_gene_variant ; 955.0bp to feature; MODIFIER silent_mutation Average:85.719; most accessible tissue: Minghui63 flag leaf, score: 95.838 N N N N
vg0807357132 T -> C LOC_Os08g12440-LOC_Os08g12449 intergenic_region ; MODIFIER silent_mutation Average:85.719; most accessible tissue: Minghui63 flag leaf, score: 95.838 N N N N
vg0807357132 T -> TCCCGCGTCGTTGTTTCACGGCAC LOC_Os08g12440.1 upstream_gene_variant ; 956.0bp to feature; MODIFIER silent_mutation Average:85.719; most accessible tissue: Minghui63 flag leaf, score: 95.838 N N N N
vg0807357132 T -> TCCCGCGTCGTTGTTTCACGGCAC LOC_Os08g12440-LOC_Os08g12449 intergenic_region ; MODIFIER silent_mutation Average:85.719; most accessible tissue: Minghui63 flag leaf, score: 95.838 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)
vg0807357132 T C 0.01 0.01 0.01 0.0 0.01 0.01
vg0807357132 T TCCCG* 0.4 0.45 0.39 0.48 0.39 0.28

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0807357132 NA 2.43E-46 mr1194 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
vg0807357132 NA 2.07E-10 mr1683 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
vg0807357132 8.22E-07 8.22E-07 mr1067_2 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
vg0807357132 4.12E-06 NA mr1071_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
vg0807357132 3.11E-07 9.41E-10 mr1071_2 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
vg0807357132 2.80E-06 NA mr1080_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
vg0807357132 5.07E-07 1.55E-09 mr1080_2 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
vg0807357132 NA 8.93E-08 mr1100_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
vg0807357132 2.64E-06 NA mr1203_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
vg0807357132 1.02E-06 4.78E-10 mr1203_2 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
vg0807357132 8.83E-07 NA mr1334_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
vg0807357132 1.24E-06 NA mr1334_2 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
vg0807357132 5.22E-07 6.58E-09 mr1402_2 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
vg0807357132 6.02E-06 NA mr1613_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
vg0807357132 2.21E-09 4.29E-13 mr1613_2 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
vg0807357132 3.82E-07 NA mr1619_2 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
vg0807357132 2.09E-09 2.44E-11 mr1619_2 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
vg0807357132 2.44E-06 2.79E-08 mr1795_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
vg0807357132 NA 3.69E-07 mr1913_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
vg0807357132 5.62E-10 1.43E-13 mr1962_2 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
vg0807357132 NA 9.57E-21 mr1968_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