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Detailed information for vg0232925929:

Variant ID: vg0232925929 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 32925929
Reference Allele: CAlternative Allele: T,CGTCGTTA
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATTTTAGAATGTACAGACACTCATAACGCACGCACACTCACTTCTATGAACATAACACACGCACGCACATAAACCCTATCTCTATAAGCATCTTCTCAA[C/T,CGTCGTTA]
GTCGTTACTACCGAGGCTCTTCTAAACTAGGCTACATGTACTTTCGCTCTAAACTTTAATTTTATTCTCGTTTAATTTCGTGGCCTTTGCATGCATGGAG

Reverse complement sequence

CTCCATGCATGCAAAGGCCACGAAATTAAACGAGAATAAAATTAAAGTTTAGAGCGAAAGTACATGTAGCCTAGTTTAGAAGAGCCTCGGTAGTAACGAC[G/A,TAACGACG]
TTGAGAAGATGCTTATAGAGATAGGGTTTATGTGCGTGCGTGTGTTATGTTCATAGAAGTGAGTGTGCGTGCGTTATGAGTGTCTGTACATTCTAAAATA

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 95.30% 3.90% 0.70% 0.00% CGTCGTTA: 0.08%
All Indica  2759 98.00% 1.80% 0.14% 0.00% NA
All Japonica  1512 99.40% 0.00% 0.33% 0.00% CGTCGTTA: 0.26%
Aus  269 48.00% 45.40% 6.69% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 97.60% 2.40% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.60% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 0.00% 0.79% 0.00% CGTCGTTA: 0.79%
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 88.50% 8.30% 3.12% 0.00% NA
Intermediate  90 91.10% 5.60% 3.33% 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
vg0232925929 C -> T LOC_Os02g53750-LOC_Os02g53770 intergenic_region ; MODIFIER silent_mutation Average:91.618; most accessible tissue: Zhenshan97 root, score: 96.399 N N N N
vg0232925929 C -> CGTCGTTA LOC_Os02g53750-LOC_Os02g53770 intergenic_region ; MODIFIER silent_mutation Average:91.618; most accessible tissue: Zhenshan97 root, score: 96.399 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)
vg0232925929 C CGTCG* 0.08 0.17 0.16 -0.01 0.11 0.38
vg0232925929 C T -0.08 -0.08 -0.06 -0.02 -0.04 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232925929 9.51E-06 NA mr1113 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
vg0232925929 2.50E-07 NA mr1114 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
vg0232925929 8.64E-07 NA mr1242 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
vg0232925929 NA 1.03E-07 mr1126_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
vg0232925929 NA 1.12E-10 mr1166_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
vg0232925929 NA 5.11E-07 mr1603_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
vg0232925929 NA 5.45E-09 mr1612_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
vg0232925929 NA 4.32E-06 mr1951_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