Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1124099257:

Variant ID: vg1124099257 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24099257
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


GCTTTGGACAAGGTACTTTTAGAGGTGCACAAGTAACATGTGCGGCTTCTGGCTTGCGCACTTCATGCACTATATGGTTTGATCCTTTTCTTGGTCAGTA[C/T]
TCAGGAACAGTAAACCATAATTAATTGGATGGAATGGACAGCCTAGCAGGCTAGCATAAGACACAATATATCTATCATTTTCTCACCAACTAGCCAATAA

Reverse complement sequence

TTATTGGCTAGTTGGTGAGAAAATGATAGATATATTGTGTCTTATGCTAGCCTGCTAGGCTGTCCATTCCATCCAATTAATTATGGTTTACTGTTCCTGA[G/A]
TACTGACCAAGAAAAGGATCAAACCATATAGTGCATGAAGTGCGCAAGCCAGAAGCCGCACATGTTACTTGTGCACCTCTAAAAGTACCTTGTCCAAAGC

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 80.20% 19.70% 0.11% 0.00% NA
All Indica  2759 86.20% 13.70% 0.04% 0.00% NA
All Japonica  1512 69.40% 30.40% 0.20% 0.00% NA
Aus  269 93.30% 6.70% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 83.70% 16.30% 0.00% 0.00% NA
Indica Intermediate  786 83.10% 16.80% 0.13% 0.00% NA
Temperate Japonica  767 85.00% 14.90% 0.13% 0.00% NA
Tropical Japonica  504 51.40% 48.40% 0.20% 0.00% NA
Japonica Intermediate  241 57.70% 41.90% 0.41% 0.00% NA
VI/Aromatic  96 39.60% 59.40% 1.04% 0.00% NA
Intermediate  90 78.90% 21.10% 0.00% 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
vg1124099257 C -> T LOC_Os11g40430.1 downstream_gene_variant ; 2675.0bp to feature; MODIFIER silent_mutation Average:68.751; most accessible tissue: Zhenshan97 root, score: 97.891 N N N N
vg1124099257 C -> T LOC_Os11g40420.1 intron_variant ; MODIFIER silent_mutation Average:68.751; most accessible tissue: Zhenshan97 root, score: 97.891 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)
vg1124099257 C T 0.06 -0.04 -0.03 -0.08 -0.03 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124099257 7.62E-06 NA mr1020 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
vg1124099257 NA 7.62E-06 mr1029 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
vg1124099257 NA 2.03E-06 mr1047 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
vg1124099257 NA 1.16E-06 mr1471 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
vg1124099257 NA 9.11E-06 mr1543 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
vg1124099257 NA 4.08E-07 mr1543 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
vg1124099257 NA 6.76E-06 mr1766 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
vg1124099257 4.67E-06 NA mr1971 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
vg1124099257 NA 4.45E-06 mr1587_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