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Detailed information for vg0434331604:

Variant ID: vg0434331604 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34331604
Reference Allele: CAlternative Allele: T,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TTATCGAGGCTGCCAGAGAGCTGATTTTCCTGTAAGCTTAGCCACCTCAACTCTGGAATCGTGTACAAGTCCTTGGGGAGGCTCCCAGTAAGGCCATTGC[C/T,A]
ATCAAGGAAGAGGTCGTTGAGCAGCTTGCACTGACCAAAGCCGGCCGGCACATCACCAGAGAAGGCATTCGCCGAGAACCGCAGGACCTTGACCGGCGAA

Reverse complement sequence

TTCGCCGGTCAAGGTCCTGCGGTTCTCGGCGAATGCCTTCTCTGGTGATGTGCCGGCCGGCTTTGGTCAGTGCAAGCTGCTCAACGACCTCTTCCTTGAT[G/A,T]
GCAATGGCCTTACTGGGAGCCTCCCCAAGGACTTGTACACGATTCCAGAGTTGAGGTGGCTAAGCTTACAGGAAAATCAGCTCTCTGGCAGCCTCGATAA

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 53.80% 45.40% 0.13% 0.59% A: 0.04%
All Indica  2759 90.10% 8.90% 0.18% 0.80% A: 0.04%
All Japonica  1512 1.30% 98.50% 0.00% 0.20% NA
Aus  269 1.10% 98.90% 0.00% 0.00% NA
Indica I  595 97.50% 2.00% 0.17% 0.34% NA
Indica II  465 94.40% 4.30% 0.22% 1.08% NA
Indica III  913 82.80% 16.20% 0.11% 0.88% NA
Indica Intermediate  786 90.30% 8.40% 0.25% 0.89% A: 0.13%
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 2.60% 97.00% 0.00% 0.40% NA
Japonica Intermediate  241 1.20% 98.30% 0.00% 0.41% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 36.70% 57.80% 1.11% 3.33% A: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0434331604 C -> DEL LOC_Os04g57660.1 N frameshift_variant Average:72.27; most accessible tissue: Minghui63 flower, score: 88.673 N N N N
vg0434331604 C -> A LOC_Os04g57660.1 missense_variant ; p.Gly176Cys; MODERATE nonsynonymous_codon ; G176C Average:72.27; most accessible tissue: Minghui63 flower, score: 88.673 probably damaging 3.575 DELETERIOUS 0.04
vg0434331604 C -> T LOC_Os04g57660.1 missense_variant ; p.Gly176Ser; MODERATE nonsynonymous_codon ; G176S Average:72.27; most accessible tissue: Minghui63 flower, score: 88.673 benign 0.826 TOLERATED 0.46

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)
vg0434331604 C A -0.02 -0.01 -0.01 -0.01 -0.01 -0.01
vg0434331604 C T 0.0 0.01 0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0434331604 NA 5.42E-06 mr1189 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
vg0434331604 NA 7.10E-06 mr1625 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
vg0434331604 NA 1.32E-06 mr1796 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
vg0434331604 4.45E-06 4.09E-06 mr1756_2 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