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Detailed information for vg1000080974:

Variant ID: vg1000080974 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 80974
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAATCTAGTACAACTACGATCTAACGGTGTAAATATTTATCCTTTTATCCGATTAATGTGGGAATTTCTAATCCCCACAGTAAACGTGGTGTCTTCTTT[T/C]
AAGGCTGTTTTAATAATATAATAGATAAATAGATAGATAGATGTGCATGGTCCTTTAGTGATGTTAGGGGCATATTAATTACAGCCGTTTACATTGTGGA

Reverse complement sequence

TCCACAATGTAAACGGCTGTAATTAATATGCCCCTAACATCACTAAAGGACCATGCACATCTATCTATCTATTTATCTATTATATTATTAAAACAGCCTT[A/G]
AAAGAAGACACCACGTTTACTGTGGGGATTAGAAATTCCCACATTAATCGGATAAAAGGATAAATATTTACACCGTTAGATCGTAGTTGTACTAGATTTT

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 50.30% 6.90% 9.80% 33.07% NA
All Indica  2759 29.70% 5.50% 11.63% 53.14% NA
All Japonica  1512 97.90% 0.20% 0.40% 1.46% NA
Aus  269 5.20% 58.70% 16.73% 19.33% NA
Indica I  595 38.20% 2.00% 9.08% 50.76% NA
Indica II  465 38.90% 3.40% 6.67% 50.97% NA
Indica III  913 24.80% 6.10% 14.35% 54.76% NA
Indica Intermediate  786 23.50% 8.80% 13.36% 54.33% NA
Temperate Japonica  767 99.20% 0.00% 0.00% 0.78% NA
Tropical Japonica  504 96.80% 0.00% 0.40% 2.78% NA
Japonica Intermediate  241 96.30% 1.20% 1.66% 0.83% NA
VI/Aromatic  96 10.40% 8.30% 78.12% 3.12% NA
Intermediate  90 57.80% 2.20% 17.78% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000080974 T -> C LOC_Os10g01080.1 3_prime_UTR_variant ; 258.0bp to feature; MODIFIER silent_mutation Average:74.595; most accessible tissue: Zhenshan97 flower, score: 93.774 N N N N
vg1000080974 T -> C LOC_Os10g01070.1 upstream_gene_variant ; 4669.0bp to feature; MODIFIER silent_mutation Average:74.595; most accessible tissue: Zhenshan97 flower, score: 93.774 N N N N
vg1000080974 T -> C LOC_Os10g01090.1 downstream_gene_variant ; 4304.0bp to feature; MODIFIER silent_mutation Average:74.595; most accessible tissue: Zhenshan97 flower, score: 93.774 N N N N
vg1000080974 T -> DEL N N silent_mutation Average:74.595; most accessible tissue: Zhenshan97 flower, score: 93.774 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)
vg1000080974 T C 0.04 -0.01 -0.03 -0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000080974 NA 2.70E-17 mr1158 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
vg1000080974 4.87E-07 7.49E-30 mr1168 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
vg1000080974 NA 1.50E-06 mr1168 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
vg1000080974 NA 6.57E-07 mr1227 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
vg1000080974 3.94E-08 7.89E-33 mr1383 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
vg1000080974 NA 2.06E-06 mr1383 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
vg1000080974 NA 1.96E-12 mr1449 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
vg1000080974 NA 1.19E-07 mr1486 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
vg1000080974 NA 1.68E-06 mr1548 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
vg1000080974 NA 1.26E-21 mr1817 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
vg1000080974 6.54E-07 5.41E-10 mr1158_2 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
vg1000080974 NA 3.86E-07 mr1158_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
vg1000080974 3.98E-10 1.42E-30 mr1168_2 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
vg1000080974 2.73E-06 6.29E-09 mr1168_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
vg1000080974 6.00E-08 1.85E-22 mr1383_2 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
vg1000080974 NA 3.05E-07 mr1486_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
vg1000080974 NA 1.47E-20 mr1817_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
vg1000080974 NA 1.30E-07 mr1855_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