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Detailed information for vg1016847259:

Variant ID: vg1016847259 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 16847259
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.22, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATTATGGGCTGTATGCCATATTTTAGATCCTATATTCCGGGGCCCCGTGGGTCACCCGCGGGTGAGCTTGTGGCCCCGCCCCCGCCCCCGCATAGTT[C/T]
CGGGGCCCCGTCCCCGCAGCCCCGCAGGTTGAAATTTCACCCCGTCCCTGTTCCCGTAGGGGCGGGTACCCGACGGGTCCCGCCCCCAACGGGGAAATTG

Reverse complement sequence

CAATTTCCCCGTTGGGGGCGGGACCCGTCGGGTACCCGCCCCTACGGGAACAGGGACGGGGTGAAATTTCAACCTGCGGGGCTGCGGGGACGGGGCCCCG[G/A]
AACTATGCGGGGGCGGGGGCGGGGCCACAAGCTCACCCGCGGGTGACCCACGGGGCCCCGGAATATAGGATCTAAAATATGGCATACAGCCCATAATCAA

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 67.50% 30.40% 0.85% 1.25% NA
All Indica  2759 96.40% 1.20% 1.05% 1.34% NA
All Japonica  1512 8.90% 90.50% 0.40% 0.20% NA
Aus  269 93.70% 0.40% 1.12% 4.83% NA
Indica I  595 94.80% 0.70% 2.18% 2.35% NA
Indica II  465 94.60% 2.80% 1.29% 1.29% NA
Indica III  913 99.00% 0.10% 0.22% 0.66% NA
Indica Intermediate  786 95.70% 1.90% 1.02% 1.40% NA
Temperate Japonica  767 2.70% 96.50% 0.65% 0.13% NA
Tropical Japonica  504 7.10% 92.30% 0.20% 0.40% NA
Japonica Intermediate  241 32.00% 68.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 1.00% 1.04% 5.21% NA
Intermediate  90 60.00% 37.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1016847259 C -> T LOC_Os10g32060.1 downstream_gene_variant ; 1465.0bp to feature; MODIFIER silent_mutation Average:83.453; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg1016847259 C -> T LOC_Os10g32070.1 downstream_gene_variant ; 146.0bp to feature; MODIFIER silent_mutation Average:83.453; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg1016847259 C -> T LOC_Os10g32080.1 downstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:83.453; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg1016847259 C -> T LOC_Os10g32060-LOC_Os10g32070 intergenic_region ; MODIFIER silent_mutation Average:83.453; most accessible tissue: Zhenshan97 panicle, score: 93.752 N N N N
vg1016847259 C -> DEL N N silent_mutation Average:83.453; most accessible tissue: Zhenshan97 panicle, score: 93.752 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)
vg1016847259 C T -0.02 -0.03 -0.02 -0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1016847259 NA 2.64E-13 mr1035 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
vg1016847259 NA 7.00E-07 mr1071 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
vg1016847259 NA 1.20E-07 mr1080 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
vg1016847259 NA 3.00E-08 mr1140 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
vg1016847259 NA 4.17E-21 mr1168 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
vg1016847259 NA 1.59E-06 mr1203 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
vg1016847259 NA 8.39E-07 mr1395 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
vg1016847259 NA 1.72E-07 mr1618 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
vg1016847259 NA 7.61E-06 mr1619 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
vg1016847259 NA 1.61E-08 mr1913 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
vg1016847259 NA 2.41E-13 mr1035_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
vg1016847259 NA 5.56E-08 mr1071_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
vg1016847259 NA 1.60E-08 mr1080_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
vg1016847259 NA 7.45E-06 mr1100_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
vg1016847259 NA 2.92E-08 mr1203_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
vg1016847259 NA 9.32E-18 mr1336_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
vg1016847259 NA 1.34E-23 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
vg1016847259 NA 9.05E-06 mr1402_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
vg1016847259 NA 2.95E-25 mr1484_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
vg1016847259 NA 8.04E-09 mr1613_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
vg1016847259 NA 7.22E-26 mr1617_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
vg1016847259 NA 4.25E-08 mr1619_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
vg1016847259 NA 1.18E-17 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
vg1016847259 NA 2.80E-10 mr1913_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
vg1016847259 NA 2.50E-19 mr1945_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
vg1016847259 NA 5.42E-06 mr1962_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