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Detailed information for vg0141988740:

Variant ID: vg0141988740 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41988740
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:


TGAGCTCGTATAGCCAAAAACTCGCAAGTCCATAATCGGTGGTGGTGAGATTTGAGAGGTGCAGCCATGGCCCATTGTCCACAAGCCAAAGCAGTCTGAC[A/G]
TGAAGAGTCCGGCGGTAAGCCTGAATTGTGGCATGCCCATACCTCCTGAGGACTGGATCACCAGCTTTCCAACCCACCGAACTGACCATGGCGGAGATCC

Reverse complement sequence

GGATCTCCGCCATGGTCAGTTCGGTGGGTTGGAAAGCTGGTGATCCAGTCCTCAGGAGGTATGGGCATGCCACAATTCAGGCTTACCGCCGGACTCTTCA[T/C]
GTCAGACTGCTTTGGCTTGTGGACAATGGGCCATGGCTGCACCTCTCAAATCTCACCACCACCGATTATGGACTTGCGAGTTTTTGGCTATACGAGCTCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.70% 31.80% 0.38% 14.09% NA
All Indica  2759 52.10% 25.80% 0.65% 21.49% NA
All Japonica  1512 51.10% 44.80% 0.00% 4.10% NA
Aus  269 67.30% 32.00% 0.00% 0.74% NA
Indica I  595 27.60% 43.00% 1.01% 28.40% NA
Indica II  465 78.30% 11.60% 0.86% 9.25% NA
Indica III  913 58.10% 18.10% 0.33% 23.55% NA
Indica Intermediate  786 48.20% 30.00% 0.64% 21.12% NA
Temperate Japonica  767 19.90% 80.10% 0.00% 0.00% NA
Tropical Japonica  504 85.50% 2.40% 0.00% 12.10% NA
Japonica Intermediate  241 78.00% 21.60% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 64.40% 25.60% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0141988740 A -> G LOC_Os01g72390.1 synonymous_variant ; p.His39His; LOW synonymous_codon Average:70.112; most accessible tissue: Minghui63 root, score: 94.207 N N N N
vg0141988740 A -> DEL LOC_Os01g72390.1 N frameshift_variant Average:70.112; most accessible tissue: Minghui63 root, score: 94.207 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)
vg0141988740 A G 0.01 0.01 0.01 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141988740 NA 1.34E-06 mr1063 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
vg0141988740 NA 5.82E-07 mr1163 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
vg0141988740 NA 1.88E-06 mr1170 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
vg0141988740 NA 1.37E-10 mr1486 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
vg0141988740 NA 1.40E-06 mr1502 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
vg0141988740 NA 3.79E-06 mr1502 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
vg0141988740 NA 4.91E-08 mr1543 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
vg0141988740 NA 7.08E-07 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
vg0141988740 NA 4.81E-06 mr1629 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
vg0141988740 NA 1.16E-06 mr1729 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
vg0141988740 NA 2.31E-06 mr1800 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
vg0141988740 NA 4.94E-06 mr1974 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
vg0141988740 NA 5.55E-07 mr1042_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
vg0141988740 NA 8.34E-06 mr1063_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
vg0141988740 NA 1.66E-06 mr1161_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
vg0141988740 2.67E-06 2.67E-06 mr1181_2 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
vg0141988740 NA 9.83E-06 mr1359_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
vg0141988740 NA 3.32E-09 mr1486_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
vg0141988740 NA 1.30E-07 mr1502_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
vg0141988740 NA 1.05E-07 mr1502_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
vg0141988740 NA 1.71E-08 mr1543_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
vg0141988740 NA 2.47E-06 mr1974_2 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