Search for Variation information by Variation ID:

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

Detailed information for vg1122663951:

Variant ID: vg1122663951 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22663951
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


CAATCCCACCTCTCATAATCTATTTACCAACCATCCCAAAAGACACTTACCAATATGGTTTAAAAACCATTAACTCTATCTCACAATTTAGCGAGTATCA[C/T]
GGCAACCGTATGATTATCGCGAGATATAATATGGTTTCTAAAACTAAAATAACCGTGATAATTGGTTTTGTACACCCTCCACCAGAGCTCGACCAAAACA

Reverse complement sequence

TGTTTTGGTCGAGCTCTGGTGGAGGGTGTACAAAACCAATTATCACGGTTATTTTAGTTTTAGAAACCATATTATATCTCGCGATAATCATACGGTTGCC[G/A]
TGATACTCGCTAAATTGTGAGATAGAGTTAATGGTTTTTAAACCATATTGGTAAGTGTCTTTTGGGATGGTTGGTAAATAGATTATGAGAGGTGGGATTG

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 45.30% 40.80% 7.15% 6.73% NA
All Indica  2759 29.20% 64.40% 1.12% 5.18% NA
All Japonica  1512 67.20% 4.00% 18.06% 10.71% NA
Aus  269 81.00% 19.00% 0.00% 0.00% NA
Indica I  595 6.70% 92.80% 0.34% 0.17% NA
Indica II  465 34.60% 62.40% 0.43% 2.58% NA
Indica III  913 41.20% 43.70% 2.08% 13.03% NA
Indica Intermediate  786 29.30% 68.30% 1.02% 1.40% NA
Temperate Japonica  767 74.20% 6.00% 15.25% 4.56% NA
Tropical Japonica  504 62.90% 2.00% 19.84% 15.28% NA
Japonica Intermediate  241 53.90% 2.10% 23.24% 20.75% NA
VI/Aromatic  96 63.50% 1.00% 29.17% 6.25% NA
Intermediate  90 44.40% 41.10% 6.67% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122663951 C -> T LOC_Os11g38250.1 upstream_gene_variant ; 3736.0bp to feature; MODIFIER silent_mutation Average:84.87; most accessible tissue: Callus, score: 94.391 N N N N
vg1122663951 C -> T LOC_Os11g38260.1 downstream_gene_variant ; 1609.0bp to feature; MODIFIER silent_mutation Average:84.87; most accessible tissue: Callus, score: 94.391 N N N N
vg1122663951 C -> T LOC_Os11g38280.1 downstream_gene_variant ; 2080.0bp to feature; MODIFIER silent_mutation Average:84.87; most accessible tissue: Callus, score: 94.391 N N N N
vg1122663951 C -> T LOC_Os11g38270.1 intron_variant ; MODIFIER silent_mutation Average:84.87; most accessible tissue: Callus, score: 94.391 N N N N
vg1122663951 C -> DEL N N silent_mutation Average:84.87; most accessible tissue: Callus, score: 94.391 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)
vg1122663951 C T -0.02 -0.01 0.0 0.0 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122663951 NA 5.02E-08 mr1220 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
vg1122663951 NA 6.12E-06 mr1318 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
vg1122663951 NA 1.83E-06 mr1534 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
vg1122663951 NA 5.22E-06 mr1691 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
vg1122663951 NA 4.69E-06 mr1705 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
vg1122663951 NA 1.19E-06 mr1728 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
vg1122663951 NA 2.00E-06 mr1458_2 Jap_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
vg1122663951 NA 1.32E-09 mr1751_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
vg1122663951 NA 1.19E-06 mr1765_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