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Detailed information for vg1019958512:

Variant ID: vg1019958512 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 19958512
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTGGCTAATTTTTTTAAGTATATTCGGATACATATTTATATTTAAAGTATTAAATATAATCTAATAATAAAATAAATTATAGATTCCGCCTGTAAACT[A/G]
CAAGACGAATTTATTAAGTCTAATTAATCCGTCATTAGTAAATATTTACTGTAGCATTACATTGTCAAATAATGACGTAATTAGGCTCAAAAGATTTGTC

Reverse complement sequence

GACAAATCTTTTGAGCCTAATTACGTCATTATTTGACAATGTAATGCTACAGTAAATATTTACTAATGACGGATTAATTAGACTTAATAAATTCGTCTTG[T/C]
AGTTTACAGGCGGAATCTATAATTTATTTTATTATTAGATTATATTTAATACTTTAAATATAAATATGTATCCGAATATACTTAAAAAAATTAGCCAAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.80% 27.10% 8.13% 4.97% NA
All Indica  2759 78.40% 2.80% 11.96% 6.81% NA
All Japonica  1512 19.60% 77.30% 1.65% 1.46% NA
Aus  269 81.00% 3.30% 8.55% 7.06% NA
Indica I  595 72.60% 2.70% 18.49% 6.22% NA
Indica II  465 79.40% 4.30% 10.97% 5.38% NA
Indica III  913 81.10% 2.20% 7.89% 8.87% NA
Indica Intermediate  786 79.10% 2.80% 12.34% 5.73% NA
Temperate Japonica  767 3.30% 96.10% 0.65% 0.00% NA
Tropical Japonica  504 47.80% 45.20% 3.57% 3.37% NA
Japonica Intermediate  241 12.40% 84.60% 0.83% 2.07% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 65.60% 21.10% 6.67% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1019958512 A -> G LOC_Os10g37260.1 upstream_gene_variant ; 1150.0bp to feature; MODIFIER silent_mutation Average:61.001; most accessible tissue: Zhenshan97 root, score: 83.259 N N N N
vg1019958512 A -> G LOC_Os10g37270.1 upstream_gene_variant ; 3151.0bp to feature; MODIFIER silent_mutation Average:61.001; most accessible tissue: Zhenshan97 root, score: 83.259 N N N N
vg1019958512 A -> G LOC_Os10g37280.1 upstream_gene_variant ; 4230.0bp to feature; MODIFIER silent_mutation Average:61.001; most accessible tissue: Zhenshan97 root, score: 83.259 N N N N
vg1019958512 A -> G LOC_Os10g37260-LOC_Os10g37270 intergenic_region ; MODIFIER silent_mutation Average:61.001; most accessible tissue: Zhenshan97 root, score: 83.259 N N N N
vg1019958512 A -> DEL N N silent_mutation Average:61.001; most accessible tissue: Zhenshan97 root, score: 83.259 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)
vg1019958512 A G 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
vg1019958512 NA 6.90E-06 mr1125 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
vg1019958512 NA 8.67E-19 mr1308 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
vg1019958512 NA 1.26E-09 mr1308 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
vg1019958512 NA 3.21E-09 mr1368 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
vg1019958512 NA 7.84E-07 mr1422 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
vg1019958512 NA 4.70E-08 mr1509 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
vg1019958512 NA 5.34E-06 mr1558 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
vg1019958512 NA 9.78E-07 mr1578 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
vg1019958512 NA 5.45E-22 mr1584 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
vg1019958512 NA 1.31E-07 mr1584 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
vg1019958512 NA 2.78E-45 mr1771 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
vg1019958512 NA 5.74E-41 mr1784 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
vg1019958512 NA 5.23E-13 mr1853 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
vg1019958512 NA 1.08E-25 mr1862 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
vg1019958512 NA 3.89E-21 mr1308_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
vg1019958512 NA 1.62E-07 mr1308_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
vg1019958512 NA 2.23E-21 mr1361_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
vg1019958512 NA 2.90E-10 mr1361_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
vg1019958512 NA 1.42E-34 mr1368_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
vg1019958512 1.63E-06 NA mr1558_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
vg1019958512 NA 2.03E-09 mr1558_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
vg1019958512 NA 2.86E-28 mr1584_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
vg1019958512 3.16E-07 5.08E-11 mr1623_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
vg1019958512 NA 1.72E-26 mr1653_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
vg1019958512 NA 1.35E-08 mr1653_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
vg1019958512 NA 7.04E-43 mr1771_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
vg1019958512 NA 1.12E-47 mr1784_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
vg1019958512 NA 1.56E-41 mr1862_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
vg1019958512 NA 2.14E-08 mr1879_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
vg1019958512 NA 4.06E-07 mr1905_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