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Detailed information for vg0628129354:

Variant ID: vg0628129354 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 28129354
Reference Allele: TTCAlternative Allele: CTC,T
Primary Allele: CTCSecondary Allele: TTC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTCAATAGTATGTCTACATGGGTATCTATAGCTCTCTAATGCATTGCCTTGTTTTTCTCTATAGACTATCTCCAGGTTAGTAGATAGCTTTGCTCTCT[TTC/CTC,T]
TTCATTTAATCTCTTCCAAGTGGAAAAATATGTTGACATATATTTCTTATAAAGAGCCTATAAATAACCATTGCGGGTGCCCTTAGCCAAAGCGACAAAA

Reverse complement sequence

TTTTGTCGCTTTGGCTAAGGGCACCCGCAATGGTTATTTATAGGCTCTTTATAAGAAATATATGTCAACATATTTTTCCACTTGGAAGAGATTAAATGAA[GAA/GAG,A]
AGAGAGCAAAGCTATCTACTAACCTGGAGATAGTCTATAGAGAAAAACAAGGCAATGCATTAGAGAGCTATAGATACCCATGTAGACATACTATTGAGAT

Allele Frequencies:

Populations Population SizeFrequency of CTC(primary allele) Frequency of TTC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.70% 7.90% 1.33% 0.00% T: 0.04%
All Indica  2759 99.70% 0.20% 0.00% 0.00% T: 0.07%
All Japonica  1512 72.10% 24.00% 3.90% 0.00% NA
Aus  269 98.10% 1.10% 0.74% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.30% 0.00% 0.00% T: 0.25%
Temperate Japonica  767 49.50% 44.50% 6.00% 0.00% NA
Tropical Japonica  504 97.80% 1.20% 0.99% 0.00% NA
Japonica Intermediate  241 90.00% 6.60% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 4.40% 2.22% 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
vg0628129354 TTC -> T LOC_Os06g46366.1 upstream_gene_variant ; 4446.0bp to feature; MODIFIER silent_mutation Average:84.085; most accessible tissue: Minghui63 root, score: 95.998 N N N N
vg0628129354 TTC -> T LOC_Os06g46360.1 intron_variant ; MODIFIER silent_mutation Average:84.085; most accessible tissue: Minghui63 root, score: 95.998 N N N N
vg0628129354 TTC -> CTC LOC_Os06g46366.1 upstream_gene_variant ; 4447.0bp to feature; MODIFIER silent_mutation Average:84.085; most accessible tissue: Minghui63 root, score: 95.998 N N N N
vg0628129354 TTC -> CTC LOC_Os06g46360.1 intron_variant ; MODIFIER silent_mutation Average:84.085; most accessible tissue: Minghui63 root, score: 95.998 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)
vg0628129354 TTC CTC 0.01 0.0 0.0 0.01 -0.01 -0.01
vg0628129354 TTC T -0.55 -0.26 -0.14 0.12 -0.05 -0.39

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0628129354 NA 5.50E-08 mr1053 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
vg0628129354 NA 4.29E-07 mr1058 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
vg0628129354 NA 1.08E-06 mr1187 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
vg0628129354 NA 3.05E-12 mr1233 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
vg0628129354 NA 6.57E-14 mr1270 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
vg0628129354 NA 1.09E-09 mr1321 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
vg0628129354 NA 4.61E-06 mr1331 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
vg0628129354 NA 1.25E-06 mr1345 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
vg0628129354 NA 2.18E-10 mr1379 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
vg0628129354 NA 9.07E-06 mr1432 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
vg0628129354 NA 7.74E-18 mr1552 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
vg0628129354 NA 1.90E-10 mr1578 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
vg0628129354 NA 1.82E-11 mr1609 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
vg0628129354 NA 2.61E-11 mr1696 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
vg0628129354 NA 6.61E-17 mr1700 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
vg0628129354 NA 3.14E-06 mr1748 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
vg0628129354 NA 1.07E-06 mr1756 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
vg0628129354 NA 1.94E-11 mr1883 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
vg0628129354 NA 1.22E-17 mr1916 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
vg0628129354 3.06E-06 7.86E-07 mr1946 Ind_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
vg0628129354 NA 1.97E-12 mr1189_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
vg0628129354 NA 4.19E-11 mr1338_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
vg0628129354 NA 3.00E-10 mr1649_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
vg0628129354 NA 9.22E-06 mr1977_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