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Detailed information for vg0138183984:

Variant ID: vg0138183984 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 38183984
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAAAAGTTTTTTTTAAAAAAAGCTATCTATCTATGCCTTTTTTCCCCGACAAATCGTATTTTTAAAAATGTGGCACGAATAAACCGATGATAACATGT[C/T]
CATGTTAGCTTATTTAAGCGTTTGTACTGTATTTCTCAAAAAAACATATTATTAGTTTGACCAGTAGTTGACACTTTTCTTTCCGAGGAAACTTTAGTAC

Reverse complement sequence

GTACTAAAGTTTCCTCGGAAAGAAAAGTGTCAACTACTGGTCAAACTAATAATATGTTTTTTTGAGAAATACAGTACAAACGCTTAAATAAGCTAACATG[G/A]
ACATGTTATCATCGGTTTATTCGTGCCACATTTTTAAAAATACGATTTGTCGGGGAAAAAAGGCATAGATAGATAGCTTTTTTTAAAAAAAACTTTTTGT

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 82.50% 14.40% 3.13% 0.00% NA
All Indica  2759 98.60% 1.40% 0.04% 0.00% NA
All Japonica  1512 49.40% 41.10% 9.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 95.40% 4.50% 0.13% 0.00% NA
Temperate Japonica  767 48.10% 37.70% 14.21% 0.00% NA
Tropical Japonica  504 39.70% 56.30% 3.97% 0.00% NA
Japonica Intermediate  241 73.90% 20.30% 5.81% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 77.80% 17.80% 4.44% 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
vg0138183984 C -> T LOC_Os01g65760-LOC_Os01g65770 intergenic_region ; MODIFIER silent_mutation Average:69.71; most accessible tissue: Minghui63 root, score: 93.631 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)
vg0138183984 C T -0.08 -0.02 -0.03 -0.01 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0138183984 4.39E-06 NA mr1135 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
vg0138183984 NA 5.14E-13 mr1641 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
vg0138183984 1.08E-06 NA mr1517_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
vg0138183984 NA 8.44E-06 mr1517_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