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Detailed information for vg0205491231:

Variant ID: vg0205491231 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5491231
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.19, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCCCATATTATTCACGGACACGAGCAGATAGGGGAGAAATAGCACGTAGGAGGTGACGAGGATGAGGGGCGGGGCGAGGTACCCAGCCGGGGAGAGCA[C/T]
ACAAGGGAAGCATATGGGATCCGGCAAGGCCTCCCACGAGCACCCATCGAGCGTGTGGCGGCCGTCCGCCGTTGCCACCACCGTGGCCCGGGACAGGTCG

Reverse complement sequence

CGACCTGTCCCGGGCCACGGTGGTGGCAACGGCGGACGGCCGCCACACGCTCGATGGGTGCTCGTGGGAGGCCTTGCCGGATCCCATATGCTTCCCTTGT[G/A]
TGCTCTCCCCGGCTGGGTACCTCGCCCCGCCCCTCATCCTCGTCACCTCCTACGTGCTATTTCTCCCCTATCTGCTCGTGTCCGTGAATAATATGGGCAA

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 81.80% 17.90% 0.28% 0.04% NA
All Indica  2759 85.10% 14.50% 0.33% 0.07% NA
All Japonica  1512 94.00% 5.80% 0.13% 0.00% NA
Aus  269 7.10% 92.90% 0.00% 0.00% NA
Indica I  595 98.70% 1.20% 0.00% 0.17% NA
Indica II  465 68.80% 30.80% 0.43% 0.00% NA
Indica III  913 87.10% 12.60% 0.33% 0.00% NA
Indica Intermediate  786 82.30% 17.00% 0.51% 0.13% NA
Temperate Japonica  767 97.00% 2.70% 0.26% 0.00% NA
Tropical Japonica  504 88.10% 11.90% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 86.50% 2.08% 0.00% NA
Intermediate  90 72.20% 27.80% 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
vg0205491231 C -> T LOC_Os02g10450.1 missense_variant ; p.Val195Met; MODERATE nonsynonymous_codon ; V195M Average:90.308; most accessible tissue: Zhenshan97 young leaf, score: 93.924 unknown unknown TOLERATED 0.23
vg0205491231 C -> DEL LOC_Os02g10450.1 N frameshift_variant Average:90.308; most accessible tissue: Zhenshan97 young leaf, score: 93.924 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)
vg0205491231 C T -0.01 -0.01 -0.02 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205491231 NA 9.58E-07 mr1032 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
vg0205491231 NA 3.34E-06 mr1164 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
vg0205491231 NA 1.43E-06 mr1165 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
vg0205491231 NA 8.39E-09 mr1170 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
vg0205491231 NA 3.38E-06 mr1380 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
vg0205491231 NA 3.47E-07 mr1478 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
vg0205491231 NA 6.31E-06 mr1553 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
vg0205491231 NA 1.05E-06 mr1561 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
vg0205491231 NA 4.68E-07 mr1158_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
vg0205491231 NA 1.18E-07 mr1170_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
vg0205491231 NA 4.56E-07 mr1619_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