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Detailed information for vg0141604372:

Variant ID: vg0141604372 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41604372
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.36, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGGCCGTCGGCGGGAGGGTTCGCGGCGAACGTGGAGAACGCGAGGAATCACAACCAGGGCGTGATCGACAACGTCAAGAACGGGACGCCGAAGCGGCC[C/T]
GGGCAGCTGGAGACGTACGTGTTCGCCATGTTCAACGAGAACCAGAAGCCCGGGGATGAGACCGAGAGGCATTTTGGGCTCTTCAATCCTGACAAGACGC

Reverse complement sequence

GCGTCTTGTCAGGATTGAAGAGCCCAAAATGCCTCTCGGTCTCATCCCCGGGCTTCTGGTTCTCGTTGAACATGGCGAACACGTACGTCTCCAGCTGCCC[G/A]
GGCCGCTTCGGCGTCCCGTTCTTGACGTTGTCGATCACGCCCTGGTTGTGATTCCTCGCGTTCTCCACGTTCGCCGCGAACCCTCCCGCCGACGGCCACC

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 57.80% 32.10% 8.21% 1.84% NA
All Indica  2759 42.70% 40.60% 13.59% 3.12% NA
All Japonica  1512 98.40% 1.20% 0.40% 0.00% NA
Aus  269 2.20% 96.70% 1.12% 0.00% NA
Indica I  595 29.60% 54.80% 8.07% 7.56% NA
Indica II  465 68.40% 12.00% 18.92% 0.65% NA
Indica III  913 29.60% 51.90% 16.10% 2.41% NA
Indica Intermediate  786 52.50% 33.70% 11.70% 2.04% NA
Temperate Japonica  767 99.50% 0.40% 0.13% 0.00% NA
Tropical Japonica  504 98.40% 1.20% 0.40% 0.00% NA
Japonica Intermediate  241 95.00% 3.70% 1.24% 0.00% NA
VI/Aromatic  96 5.20% 94.80% 0.00% 0.00% NA
Intermediate  90 63.30% 31.10% 4.44% 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
vg0141604372 C -> T LOC_Os01g71830.1 synonymous_variant ; p.Pro275Pro; LOW synonymous_codon Average:58.893; most accessible tissue: Zhenshan97 root, score: 95.304 N N N N
vg0141604372 C -> DEL LOC_Os01g71830.1 N frameshift_variant Average:58.893; most accessible tissue: Zhenshan97 root, score: 95.304 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)
vg0141604372 C T 0.05 -0.02 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141604372 NA 3.27E-22 Plant_height 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
vg0141604372 NA 1.82E-16 Plant_height Ind_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
vg0141604372 NA 4.38E-06 mr1192 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
vg0141604372 NA 4.25E-07 mr1574 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
vg0141604372 NA 6.52E-16 mr1765 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
vg0141604372 NA 7.39E-09 mr1265_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
vg0141604372 NA 8.45E-06 mr1265_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
vg0141604372 NA 8.06E-08 mr1268_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
vg0141604372 NA 1.67E-10 mr1327_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
vg0141604372 NA 1.15E-10 mr1327_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
vg0141604372 NA 1.89E-12 mr1378_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
vg0141604372 NA 7.87E-08 mr1378_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
vg0141604372 NA 6.02E-06 mr1522_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
vg0141604372 NA 4.60E-07 mr1528_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
vg0141604372 NA 1.88E-18 mr1817_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
vg0141604372 NA 2.36E-06 mr1860_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
vg0141604372 NA 3.99E-07 mr1971_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
vg0141604372 NA 5.20E-07 mr1977_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