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Detailed information for vg0139108098:

Variant ID: vg0139108098 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 39108098
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTATTCTTTGACTGTTTAGCCCATCCGATGAGAGACTTACTTAATTGACAGCATAAAATTAAACCTTCCCCTTCACAGAATCTCTTTACCACAAGTCAC[C/T]
ATCTGTCGTGCTTTGTTCTTTCTGCAGGCGGTGGTGGATCATGCCGACTTTTAATCACGCATTCACGCATGTAGTTTTCCAACGGCGACTCCGGCGATCC

Reverse complement sequence

GGATCGCCGGAGTCGCCGTTGGAAAACTACATGCGTGAATGCGTGATTAAAAGTCGGCATGATCCACCACCGCCTGCAGAAAGAACAAAGCACGACAGAT[G/A]
GTGACTTGTGGTAAAGAGATTCTGTGAAGGGGAAGGTTTAATTTTATGCTGTCAATTAAGTAAGTCTCTCATCGGATGGGCTAAACAGTCAAAGAATAAA

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 95.70% 4.30% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 90.00% 10.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 88.80% 11.20% 0.00% 0.00% NA
Tropical Japonica  504 88.50% 11.50% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0139108098 C -> T LOC_Os01g67360.1 upstream_gene_variant ; 2334.0bp to feature; MODIFIER silent_mutation Average:78.866; most accessible tissue: Zhenshan97 flag leaf, score: 92.238 N N N N
vg0139108098 C -> T LOC_Os01g67360-LOC_Os01g67364 intergenic_region ; MODIFIER silent_mutation Average:78.866; most accessible tissue: Zhenshan97 flag leaf, score: 92.238 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)
vg0139108098 C T 0.06 0.16 0.2 0.02 0.09 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0139108098 NA 5.50E-08 mr1028 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
vg0139108098 7.29E-07 7.29E-07 mr1369 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
vg0139108098 NA 5.53E-08 mr1453 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
vg0139108098 NA 5.19E-06 mr1510 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
vg0139108098 NA 5.39E-06 mr1648 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
vg0139108098 NA 1.25E-08 mr1652 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
vg0139108098 NA 1.66E-06 mr1968 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
vg0139108098 NA 3.45E-06 mr1164_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