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Detailed information for vg1017015504:

Variant ID: vg1017015504 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 17015504
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.11, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:


GACATGAGGAAGTGGAAGAAGACGCTCTTGGAGCACGTGGCATGCTGCACGACGGGGCAAGGCGCGACGGCGGGAGATGAGGAGGCCCGGAGGCCGGCGA[T/C]
GCGATGGGGGCGACGAGGCGGCGCGTCCGGCCGCCGATAGGGGAGAAGCGCAGTGGCGCCGCTCGACTGCGCTCGGCCTGCCGCGTCTGCGCCGGCTTGC

Reverse complement sequence

GCAAGCCGGCGCAGACGCGGCAGGCCGAGCGCAGTCGAGCGGCGCCACTGCGCTTCTCCCCTATCGGCGGCCGGACGCGCCGCCTCGTCGCCCCCATCGC[A/G]
TCGCCGGCCTCCGGGCCTCCTCATCTCCCGCCGTCGCGCCTTGCCCCGTCGTGCAGCATGCCACGTGCTCCAAGAGCGTCTTCTTCCACTTCCTCATGTC

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 65.80% 19.40% 5.42% 9.37% NA
All Indica  2759 85.00% 0.80% 6.34% 7.79% NA
All Japonica  1512 35.80% 57.90% 2.05% 4.17% NA
Aus  269 51.30% 0.00% 14.87% 33.83% NA
Indica I  595 77.80% 0.20% 12.10% 9.92% NA
Indica II  465 78.10% 2.80% 7.74% 11.40% NA
Indica III  913 92.00% 0.00% 2.63% 5.37% NA
Indica Intermediate  786 86.50% 1.10% 5.47% 6.87% NA
Temperate Japonica  767 3.00% 95.30% 0.91% 0.78% NA
Tropical Japonica  504 85.10% 8.50% 1.59% 4.76% NA
Japonica Intermediate  241 37.30% 42.30% 6.64% 13.69% NA
VI/Aromatic  96 32.30% 1.00% 0.00% 66.67% NA
Intermediate  90 61.10% 16.70% 11.11% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1017015504 T -> C LOC_Os10g32470.1 upstream_gene_variant ; 4489.0bp to feature; MODIFIER silent_mutation Average:88.445; most accessible tissue: Zhenshan97 panicle, score: 95.997 N N N N
vg1017015504 T -> C LOC_Os10g32500.1 upstream_gene_variant ; 3418.0bp to feature; MODIFIER silent_mutation Average:88.445; most accessible tissue: Zhenshan97 panicle, score: 95.997 N N N N
vg1017015504 T -> C LOC_Os10g32470-LOC_Os10g32500 intergenic_region ; MODIFIER silent_mutation Average:88.445; most accessible tissue: Zhenshan97 panicle, score: 95.997 N N N N
vg1017015504 T -> DEL N N silent_mutation Average:88.445; most accessible tissue: Zhenshan97 panicle, score: 95.997 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)
vg1017015504 T C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1017015504 NA 2.52E-08 mr1040 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
vg1017015504 NA 6.54E-19 mr1077 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
vg1017015504 3.28E-06 NA mr1112 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
vg1017015504 NA 3.21E-06 mr1156 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
vg1017015504 NA 4.94E-07 mr1157 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
vg1017015504 NA 1.10E-18 mr1179 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
vg1017015504 NA 1.49E-06 mr1179 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
vg1017015504 NA 8.32E-07 mr1229 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
vg1017015504 NA 9.89E-07 mr1252 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
vg1017015504 NA 2.51E-06 mr1263 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
vg1017015504 NA 3.37E-07 mr1271 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
vg1017015504 NA 2.51E-06 mr1451 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
vg1017015504 7.72E-06 7.72E-06 mr1494 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
vg1017015504 NA 2.45E-06 mr1495 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
vg1017015504 NA 7.69E-06 mr1520 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
vg1017015504 NA 6.03E-12 mr1539 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
vg1017015504 NA 7.98E-12 mr1539 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
vg1017015504 NA 6.13E-16 mr1540 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
vg1017015504 NA 1.50E-14 mr1540 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
vg1017015504 NA 1.34E-06 mr1543 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
vg1017015504 NA 1.62E-09 mr1580 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
vg1017015504 NA 4.34E-10 mr1624 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
vg1017015504 NA 5.58E-15 mr1732 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
vg1017015504 NA 4.39E-08 mr1733 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
vg1017015504 NA 1.22E-08 mr1770 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
vg1017015504 NA 8.49E-07 mr1826 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
vg1017015504 4.81E-06 4.81E-06 mr1836 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
vg1017015504 NA 6.85E-06 mr1871 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
vg1017015504 NA 4.01E-11 mr1055_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
vg1017015504 NA 1.71E-07 mr1156_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
vg1017015504 NA 9.70E-13 mr1390_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