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Detailed information for vg0604757294:

Variant ID: vg0604757294 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4757294
Reference Allele: TAlternative Allele: C,G
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.09, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAAGGAAGAGAGAGAGGGTGTGAAAAATTTAAAGTGGACGGGAGGAAAAAAGGGGAAAGAGAGTGTGAAAAATTTGAAATGGGTAGGAGGGAAATGAA[T/C,G]
GAGGTATTTTCCTGTACAGTCCACTTAAAAAACCTGTACGAGATAATCGATTATCTCGTGCGGTCCGCATAACACAACCGCATGGGATAATAGAAATTAT

Reverse complement sequence

ATAATTTCTATTATCCCATGCGGTTGTGTTATGCGGACCGCACGAGATAATCGATTATCTCGTACAGGTTTTTTAAGTGGACTGTACAGGAAAATACCTC[A/G,C]
TTCATTTCCCTCCTACCCATTTCAAATTTTTCACACTCTCTTTCCCCTTTTTTCCTCCCGTCCACTTTAAATTTTTCACACCCTCTCTCTCTTCCTTTTT

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 74.40% 25.50% 0.11% 0.00% NA
All Indica  2759 87.30% 12.70% 0.00% 0.00% NA
All Japonica  1512 64.20% 35.60% 0.20% 0.00% NA
Aus  269 4.50% 95.50% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 69.20% 30.80% 0.00% 0.00% NA
Indica III  913 90.80% 9.20% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 15.30% 0.00% 0.00% NA
Temperate Japonica  767 85.90% 14.00% 0.13% 0.00% NA
Tropical Japonica  504 28.00% 71.60% 0.40% 0.00% NA
Japonica Intermediate  241 71.00% 29.00% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 62.20% 35.60% 2.22% 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
vg0604757294 T -> C LOC_Os06g09410.1 synonymous_variant ; p.Asn245Asn; LOW synonymous_codon Average:72.724; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N
vg0604757294 T -> G LOC_Os06g09410.1 missense_variant ; p.Asn245Lys; MODERATE N Average:72.724; most accessible tissue: Zhenshan97 panicle, score: 86.058 N N N N
vg0604757294 T -> G LOC_Os06g09420.1 upstream_gene_variant ; 4710.0bp to feature; MODIFIER N Average:72.724; most accessible tissue: Zhenshan97 panicle, score: 86.058 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)
vg0604757294 T C 0.02 0.01 0.02 0.02 0.02 0.01
vg0604757294 T G -0.01 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604757294 NA 6.46E-06 mr1070 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
vg0604757294 7.44E-06 NA mr1137 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
vg0604757294 2.53E-06 8.87E-11 mr1137 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
vg0604757294 NA 4.81E-12 mr1141 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
vg0604757294 NA 4.67E-06 mr1521 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
vg0604757294 NA 1.39E-09 mr1617 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
vg0604757294 NA 2.81E-06 mr1903 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
vg0604757294 NA 2.29E-08 mr1137_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
vg0604757294 NA 1.16E-11 mr1141_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
vg0604757294 NA 2.74E-06 mr1320_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