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Detailed information for vg0810506618:

Variant ID: vg0810506618 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 10506618
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.03, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


CCCACGGGTGATAATTAGGGGGCTGTTTGGTTTCCAGGACTTATTCCAAGTACCTGTCACATCGGATATTTGGACACTAATTTGGAGTATTAAACATACA[T/C]
TAATTATAAAACCCATTTCATAAGCTTAGACTAATTCGCGAGACGAATCTTTTGAATCTAATTACGCCATGATTTTGACAATGTGATGCTACAGTAAAGT

Reverse complement sequence

ACTTTACTGTAGCATCACATTGTCAAAATCATGGCGTAATTAGATTCAAAAGATTCGTCTCGCGAATTAGTCTAAGCTTATGAAATGGGTTTTATAATTA[A/G]
TGTATGTTTAATACTCCAAATTAGTGTCCAAATATCCGATGTGACAGGTACTTGGAATAAGTCCTGGAAACCAAACAGCCCCCTAATTATCACCCGTGGG

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 23.10% 20.50% 0.44% 55.97% NA
All Indica  2759 12.30% 5.80% 0.54% 81.44% NA
All Japonica  1512 41.80% 52.10% 0.00% 6.08% NA
Aus  269 1.10% 0.40% 0.37% 98.14% NA
Indica I  595 4.20% 5.20% 0.17% 90.42% NA
Indica II  465 9.50% 1.90% 0.86% 87.74% NA
Indica III  913 20.90% 10.10% 0.44% 68.57% NA
Indica Intermediate  786 9.90% 3.40% 0.76% 85.88% NA
Temperate Japonica  767 9.40% 86.30% 0.00% 4.30% NA
Tropical Japonica  504 83.50% 10.30% 0.00% 6.15% NA
Japonica Intermediate  241 57.70% 30.70% 0.00% 11.62% NA
VI/Aromatic  96 93.80% 0.00% 1.04% 5.21% NA
Intermediate  90 33.30% 21.10% 4.44% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0810506618 T -> C LOC_Os08g17160.1 upstream_gene_variant ; 1506.0bp to feature; MODIFIER silent_mutation Average:93.732; most accessible tissue: Minghui63 panicle, score: 97.163 N N N N
vg0810506618 T -> C LOC_Os08g17150.1 downstream_gene_variant ; 2345.0bp to feature; MODIFIER silent_mutation Average:93.732; most accessible tissue: Minghui63 panicle, score: 97.163 N N N N
vg0810506618 T -> C LOC_Os08g17150-LOC_Os08g17160 intergenic_region ; MODIFIER silent_mutation Average:93.732; most accessible tissue: Minghui63 panicle, score: 97.163 N N N N
vg0810506618 T -> DEL N N silent_mutation Average:93.732; most accessible tissue: Minghui63 panicle, score: 97.163 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)
vg0810506618 T C -0.02 -0.04 -0.03 -0.01 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0810506618 NA 5.55E-06 mr1045 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
vg0810506618 NA 6.82E-07 mr1238 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
vg0810506618 NA 2.78E-07 mr1309 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
vg0810506618 NA 1.08E-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
vg0810506618 3.17E-06 3.17E-06 mr1566 Ind_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
vg0810506618 NA 4.77E-08 mr1668 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
vg0810506618 NA 5.55E-06 mr1775 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
vg0810506618 NA 7.42E-08 mr1864 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
vg0810506618 1.46E-06 1.46E-06 mr1900 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
vg0810506618 NA 3.58E-07 mr1042_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
vg0810506618 NA 7.42E-06 mr1045_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
vg0810506618 NA 7.97E-06 mr1206_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
vg0810506618 NA 1.11E-07 mr1229_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
vg0810506618 NA 4.19E-06 mr1404_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
vg0810506618 NA 7.35E-09 mr1521_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
vg0810506618 NA 5.67E-09 mr1543_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
vg0810506618 NA 5.18E-07 mr1570_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
vg0810506618 NA 6.70E-06 mr1596_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
vg0810506618 NA 1.52E-11 mr1611_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
vg0810506618 NA 6.78E-09 mr1671_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
vg0810506618 NA 3.46E-09 mr1742_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
vg0810506618 NA 1.52E-08 mr1746_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
vg0810506618 NA 1.74E-08 mr1794_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
vg0810506618 NA 1.99E-08 mr1880_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