Search for Variation information by Variation ID:

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

Detailed information for vg0105772813:

Variant ID: vg0105772813 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5772813
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.16, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TACTGGACTTGGAATCAAATCGACGATTAGCACACTAAGAGCAAGTTCAATAGTATAGCTAACTACTAGCTCCAATTCATCTATAGCCAATTTAATAGCT[T/C]
ATTCATATAATAGTTACATACTACACTATTAATACATGGTCCCACATGTCATACACATATTGTGTCTTGGAGTCCGTGCTACAGCTGGCTATAAATCTGT

Reverse complement sequence

ACAGATTTATAGCCAGCTGTAGCACGGACTCCAAGACACAATATGTGTATGACATGTGGGACCATGTATTAATAGTGTAGTATGTAACTATTATATGAAT[A/G]
AGCTATTAAATTGGCTATAGATGAATTGGAGCTAGTAGTTAGCTATACTATTGAACTTGCTCTTAGTGTGCTAATCGTCGATTTGATTCCAAGTCCAGTA

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 58.40% 32.40% 0.15% 9.04% NA
All Indica  2759 51.20% 40.60% 0.14% 8.05% NA
All Japonica  1512 79.40% 9.10% 0.13% 11.31% NA
Aus  269 3.70% 85.50% 0.00% 10.78% NA
Indica I  595 10.10% 80.30% 0.50% 9.08% NA
Indica II  465 61.50% 38.50% 0.00% 0.00% NA
Indica III  913 73.30% 24.80% 0.00% 1.97% NA
Indica Intermediate  786 50.50% 30.30% 0.13% 19.08% NA
Temperate Japonica  767 95.60% 3.10% 0.00% 1.30% NA
Tropical Japonica  504 70.60% 6.00% 0.20% 23.21% NA
Japonica Intermediate  241 46.50% 34.90% 0.41% 18.26% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 67.80% 25.60% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0105772813 T -> DEL N N silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10800.1 upstream_gene_variant ; 4854.0bp to feature; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10830.1 upstream_gene_variant ; 487.0bp to feature; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10810.1 downstream_gene_variant ; 3351.0bp to feature; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10820.1 downstream_gene_variant ; 779.0bp to feature; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10840.1 downstream_gene_variant ; 1468.0bp to feature; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 N N N N
vg0105772813 T -> C LOC_Os01g10820-LOC_Os01g10830 intergenic_region ; MODIFIER silent_mutation Average:89.271; most accessible tissue: Minghui63 root, score: 97.765 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)
vg0105772813 T C -0.04 -0.04 -0.03 0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105772813 NA 2.57E-09 mr1829 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
vg0105772813 NA 4.94E-12 mr1902 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
vg0105772813 NA 3.90E-06 mr1024_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
vg0105772813 NA 6.26E-06 mr1155_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
vg0105772813 NA 9.38E-07 mr1159_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
vg0105772813 NA 5.11E-07 mr1229_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
vg0105772813 NA 4.58E-06 mr1236_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
vg0105772813 NA 5.84E-06 mr1236_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
vg0105772813 NA 2.14E-07 mr1252_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
vg0105772813 NA 4.32E-08 mr1299_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
vg0105772813 NA 9.10E-08 mr1482_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
vg0105772813 NA 1.34E-07 mr1727_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
vg0105772813 2.80E-06 NA mr1728_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
vg0105772813 NA 8.94E-11 mr1739_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
vg0105772813 NA 2.58E-09 mr1741_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
vg0105772813 NA 4.57E-08 mr1748_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
vg0105772813 NA 4.94E-06 mr1763_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
vg0105772813 5.93E-06 NA mr1769_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
vg0105772813 NA 2.11E-07 mr1785_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
vg0105772813 NA 1.17E-13 mr1829_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
vg0105772813 NA 1.62E-06 mr1840_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
vg0105772813 NA 3.89E-07 mr1856_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
vg0105772813 NA 4.43E-08 mr1880_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
vg0105772813 NA 9.34E-21 mr1902_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
vg0105772813 NA 1.15E-06 mr1915_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