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Detailed information for vg0917117261:

Variant ID: vg0917117261 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 17117261
Reference Allele: TCAGGGTTTGTCAlternative Allele: CCAGGGTTTGTC,T
Primary Allele: TCAGGGTTTGTCSecondary Allele: CCAGGGTTTGTC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATAAAAAAACATAATTAATATTTTATGCGTGACTTATCTTTTTAATTTTTTTTATAATTTTTTCAAATAAGACGAACGGTTAAATGTTGAAAACGGAAA[TCAGGGTTTGTC/CCAGGGTTTGTC,T]
TTTTTTTTACGGAGGGAGTACAGGCAGTACAAAAAGCAATGGTAAACGTGCCACGGGAACGAATCTTTGCTTATTAGAAGTTCTTTAGTTAGCAGTAGCA

Reverse complement sequence

TGCTACTGCTAACTAAAGAACTTCTAATAAGCAAAGATTCGTTCCCGTGGCACGTTTACCATTGCTTTTTGTACTGCCTGTACTCCCTCCGTAAAAAAAA[GACAAACCCTGA/GACAAACCCTGG,A]
TTTCCGTTTTCAACATTTAACCGTTCGTCTTATTTGAAAAAATTATAAAAAAAATTAAAAAGATAAGTCACGCATAAAATATTAATTATGTTTTTTTATC

Allele Frequencies:

Populations Population SizeFrequency of TCAGGGTTTGTC(primary allele) Frequency of CCAGGGTTTGTC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.50% 22.20% 1.44% 41.85% NA
All Indica  2759 22.30% 7.00% 1.96% 68.83% NA
All Japonica  1512 47.00% 49.50% 0.66% 2.84% NA
Aus  269 98.10% 0.40% 0.00% 1.49% NA
Indica I  595 54.80% 2.40% 0.50% 42.35% NA
Indica II  465 8.00% 6.90% 0.86% 84.30% NA
Indica III  913 3.40% 10.60% 4.05% 81.93% NA
Indica Intermediate  786 28.00% 6.20% 1.27% 64.50% NA
Temperate Japonica  767 77.10% 22.20% 0.52% 0.26% NA
Tropical Japonica  504 5.60% 85.90% 0.99% 7.54% NA
Japonica Intermediate  241 37.80% 60.60% 0.41% 1.24% NA
VI/Aromatic  96 5.20% 82.30% 3.12% 9.38% NA
Intermediate  90 41.10% 32.20% 1.11% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0917117261 TCAGGGTTTGTC -> DEL N N silent_mutation Average:69.115; most accessible tissue: Callus, score: 99.106 N N N N
vg0917117261 TCAGGGTTTGTC -> T LOC_Os09g28200-LOC_Os09g28210 intergenic_region ; MODIFIER N Average:69.115; most accessible tissue: Callus, score: 99.106 N N N N
vg0917117261 TCAGGGTTTGTC -> CCAGGGTTTGTC LOC_Os09g28200-LOC_Os09g28210 intergenic_region ; MODIFIER silent_mutation Average:69.115; most accessible tissue: Callus, score: 99.106 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)
vg0917117261 TCAGG* CCAGG* -0.02 -0.03 -0.03 0.0 -0.02 -0.02
vg0917117261 TCAGG* T -0.25 -0.26 -0.27 0.04 0.01 0.12

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0917117261 1.46E-08 NA Awn_length 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
vg0917117261 NA 3.75E-12 mr1182 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
vg0917117261 NA 8.01E-06 mr1182 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
vg0917117261 NA 5.12E-11 mr1282 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
vg0917117261 NA 5.87E-06 mr1282 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
vg0917117261 NA 1.23E-09 mr1658 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
vg0917117261 8.63E-06 NA mr1057_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
vg0917117261 NA 1.82E-07 mr1057_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
vg0917117261 NA 6.68E-14 mr1182_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
vg0917117261 NA 2.66E-06 mr1182_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
vg0917117261 NA 2.05E-11 mr1282_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
vg0917117261 NA 1.19E-07 mr1399_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
vg0917117261 NA 5.11E-07 mr1551_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
vg0917117261 NA 7.32E-11 mr1667_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
vg0917117261 6.12E-06 NA mr1679_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
vg0917117261 NA 4.00E-09 mr1681_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
vg0917117261 4.95E-06 NA mr1713_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
vg0917117261 1.30E-06 NA mr1733_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
vg0917117261 8.67E-06 NA mr1735_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
vg0917117261 1.90E-06 NA mr1757_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
vg0917117261 NA 4.44E-06 mr1980_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