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Detailed information for vg1010093642:

Variant ID: vg1010093642 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10093642
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.25, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CTATGCAGTTTAATTTACTATTCTATATGTTTCATAAATGTCATTCCATATATTCACAGGTTGGTTGGGTCTATGGATCACTGACAGAAGACGTGTTGAC[C/T]
GGACAACGGATCCATGCAGCGGGTTGGAGATCCACGCTGATGGAAATCGAACCACCAGCATTCATGGGTTGTGCACCAAATGGAGGGCCCGCCTGCCTAA

Reverse complement sequence

TTAGGCAGGCGGGCCCTCCATTTGGTGCACAACCCATGAATGCTGGTGGTTCGATTTCCATCAGCGTGGATCTCCAACCCGCTGCATGGATCCGTTGTCC[G/A]
GTCAACACGTCTTCTGTCAGTGATCCATAGACCCAACCAACCTGTGAATATATGGAATGACATTTATGAAACATATAGAATAGTAAATTAAACTGCATAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.70% 45.80% 0.11% 0.38% NA
All Indica  2759 64.80% 34.50% 0.11% 0.58% NA
All Japonica  1512 31.50% 68.30% 0.07% 0.07% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 26.90% 72.60% 0.17% 0.34% NA
Indica II  465 81.70% 16.80% 0.22% 1.29% NA
Indica III  913 79.30% 20.30% 0.11% 0.33% NA
Indica Intermediate  786 66.70% 32.70% 0.00% 0.64% NA
Temperate Japonica  767 11.50% 88.40% 0.00% 0.13% NA
Tropical Japonica  504 61.90% 37.90% 0.20% 0.00% NA
Japonica Intermediate  241 32.00% 68.00% 0.00% 0.00% NA
VI/Aromatic  96 17.70% 81.20% 1.04% 0.00% NA
Intermediate  90 42.20% 56.70% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1010093642 C -> T LOC_Os10g20090.1 synonymous_variant ; p.Thr462Thr; LOW synonymous_codon Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 N N N N
vg1010093642 C -> T LOC_Os10g20090.2 synonymous_variant ; p.Thr462Thr; LOW synonymous_codon Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 N N N N
vg1010093642 C -> T LOC_Os10g20090.3 synonymous_variant ; p.Thr462Thr; LOW synonymous_codon Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 N N N N
vg1010093642 C -> DEL LOC_Os10g20090.1 N frameshift_variant Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 N N N N
vg1010093642 C -> DEL LOC_Os10g20090.3 N frameshift_variant Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 N N N N
vg1010093642 C -> DEL LOC_Os10g20090.2 N frameshift_variant Average:89.83; most accessible tissue: Zhenshan97 root, score: 98.839 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)
vg1010093642 C T 0.07 0.11 0.03 0.03 0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010093642 NA 2.86E-19 mr1026 Ind_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
vg1010093642 4.50E-07 NA mr1118 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
vg1010093642 1.14E-06 1.46E-15 mr1118 Ind_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
vg1010093642 NA 1.84E-06 mr1120 Ind_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
vg1010093642 NA 7.66E-18 mr1161 Ind_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
vg1010093642 1.30E-06 NA mr1495 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
vg1010093642 NA 8.31E-18 mr1495 Ind_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
vg1010093642 NA 4.21E-07 mr1495 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
vg1010093642 NA 1.64E-06 mr1496 Ind_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
vg1010093642 NA 5.88E-06 mr1870 Ind_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
vg1010093642 NA 1.66E-06 mr1110_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
vg1010093642 NA 1.78E-19 mr1118_2 Ind_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
vg1010093642 NA 3.67E-06 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
vg1010093642 NA 1.11E-07 mr1120_2 Ind_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
vg1010093642 NA 3.32E-21 mr1161_2 Ind_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
vg1010093642 NA 4.53E-20 mr1495_2 Ind_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
vg1010093642 NA 1.63E-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
vg1010093642 NA 2.64E-07 mr1531_2 Ind_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
vg1010093642 NA 6.29E-07 mr1936_2 Ind_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