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Detailed information for vg0611603888:

Variant ID: vg0611603888 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11603888
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CAGAGTAGTGCAAAATAGACTATAAGTTTATAGCAATCGGAGTCCGAACGAAGTCCCGAGGATTGAATAGATGTGGGCCGTTAGATATTTTTTTTAGTCT[C/A]
TTTATATAACCAACCAAAAAAGAAAAAAAACGAACGAAAAAAAAAGAAAAAAAAAGGAGCATCGCTCCTGCAGCCCTAGCCGCGTCACCCCCTGCGTTTT

Reverse complement sequence

AAAACGCAGGGGGTGACGCGGCTAGGGCTGCAGGAGCGATGCTCCTTTTTTTTTCTTTTTTTTTCGTTCGTTTTTTTTCTTTTTTGGTTGGTTATATAAA[G/T]
AGACTAAAAAAAATATCTAACGGCCCACATCTATTCAATCCTCGGGACTTCGTTCGGACTCCGATTGCTATAAACTTATAGTCTATTTTGCACTACTCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.20% 36.40% 1.21% 6.14% NA
All Indica  2759 90.90% 5.10% 1.30% 2.72% NA
All Japonica  1512 2.00% 88.50% 0.33% 9.19% NA
Aus  269 26.40% 46.80% 3.72% 23.05% NA
Indica I  595 90.90% 6.70% 1.01% 1.34% NA
Indica II  465 87.30% 3.90% 1.72% 7.10% NA
Indica III  913 96.40% 2.50% 0.66% 0.44% NA
Indica Intermediate  786 86.50% 7.60% 2.04% 3.82% NA
Temperate Japonica  767 1.80% 93.90% 0.13% 4.17% NA
Tropical Japonica  504 2.00% 80.60% 0.79% 16.67% NA
Japonica Intermediate  241 2.50% 88.00% 0.00% 9.54% NA
VI/Aromatic  96 9.40% 82.30% 2.08% 6.25% NA
Intermediate  90 45.60% 41.10% 4.44% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611603888 C -> A LOC_Os06g20210.1 downstream_gene_variant ; 2258.0bp to feature; MODIFIER silent_mutation Average:74.85; most accessible tissue: Zhenshan97 flower, score: 88.465 N N N N
vg0611603888 C -> A LOC_Os06g20210-LOC_Os06g20230 intergenic_region ; MODIFIER silent_mutation Average:74.85; most accessible tissue: Zhenshan97 flower, score: 88.465 N N N N
vg0611603888 C -> DEL N N silent_mutation Average:74.85; most accessible tissue: Zhenshan97 flower, score: 88.465 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)
vg0611603888 C A 0.02 0.02 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611603888 NA 4.84E-06 Yield Jap_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
vg0611603888 2.41E-06 1.55E-07 mr1020 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
vg0611603888 7.34E-09 7.34E-09 mr1032 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
vg0611603888 1.63E-08 1.63E-08 mr1165 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
vg0611603888 8.34E-11 8.34E-11 mr1478 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
vg0611603888 5.22E-07 3.08E-09 mr1971 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
vg0611603888 5.65E-06 5.53E-07 mr1111_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
vg0611603888 5.10E-10 7.60E-13 mr1165_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
vg0611603888 NA 7.63E-09 mr1172_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
vg0611603888 NA 2.26E-55 mr1211_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
vg0611603888 3.70E-07 3.70E-07 mr1477_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
vg0611603888 NA 1.24E-15 mr1686_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