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Detailed information for vg0103604713:

Variant ID: vg0103604713 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 3604713
Reference Allele: CAlternative Allele: T,CCAACTTTTTTTT
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTTATCACATCACATCACATCCAAAACTTTTTTACACACATAAGTTTTCAATTTTTTTCCCAAACTTTCAACTTTTTTCAAACTTCTAACTATTTTT[C/T,CCAACTTTTTTTT]
CAGGAACTAAACACACCCGTAATGTATTACGTGTGTGCACGTTCCACTTCCAGCAGGTGGCCGGTGAGCGCGTACGTTTGGGCCAATGCAGGAGGTGGGG

Reverse complement sequence

CCCCACCTCCTGCATTGGCCCAAACGTACGCGCTCACCGGCCACCTGCTGGAAGTGGAACGTGCACACACGTAATACATTACGGGTGTGTTTAGTTCCTG[G/A,AAAAAAAAGTTGG]
AAAAATAGTTAGAAGTTTGAAAAAAGTTGAAAGTTTGGGAAAAAAATTGAAAACTTATGTGTGTAAAAAAGTTTTGGATGTGATGTGATGTGATAAAAAG

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 43.40% 21.00% 9.54% 25.65% CCAACTTTTTTTT: 0.40%
All Indica  2759 17.80% 33.20% 14.06% 34.25% CCAACTTTTTTTT: 0.69%
All Japonica  1512 95.20% 1.30% 1.59% 1.92% NA
Aus  269 8.60% 13.80% 7.06% 70.63% NA
Indica I  595 58.20% 17.30% 12.61% 11.26% CCAACTTTTTTTT: 0.67%
Indica II  465 4.70% 32.30% 16.99% 46.02% NA
Indica III  913 3.00% 43.80% 10.62% 42.39% CCAACTTTTTTTT: 0.22%
Indica Intermediate  786 12.30% 33.30% 17.43% 35.24% CCAACTTTTTTTT: 1.65%
Temperate Japonica  767 92.70% 1.80% 2.61% 2.87% NA
Tropical Japonica  504 97.80% 0.80% 0.60% 0.79% NA
Japonica Intermediate  241 97.50% 0.80% 0.41% 1.24% NA
VI/Aromatic  96 57.30% 9.40% 8.33% 25.00% NA
Intermediate  90 48.90% 11.10% 13.33% 26.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0103604713 C -> T LOC_Os01g07530.1 upstream_gene_variant ; 2502.0bp to feature; MODIFIER silent_mutation Average:84.284; most accessible tissue: Callus, score: 94.672 N N N N
vg0103604713 C -> T LOC_Os01g07530-LOC_Os01g07540 intergenic_region ; MODIFIER silent_mutation Average:84.284; most accessible tissue: Callus, score: 94.672 N N N N
vg0103604713 C -> DEL N N silent_mutation Average:84.284; most accessible tissue: Callus, score: 94.672 N N N N
vg0103604713 C -> CCAACTTTTTTTT LOC_Os01g07530.1 upstream_gene_variant ; 2503.0bp to feature; MODIFIER silent_mutation Average:84.284; most accessible tissue: Callus, score: 94.672 N N N N
vg0103604713 C -> CCAACTTTTTTTT LOC_Os01g07530-LOC_Os01g07540 intergenic_region ; MODIFIER silent_mutation Average:84.284; most accessible tissue: Callus, score: 94.672 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)
vg0103604713 C CCAAC* -0.13 -0.05 -0.06 -0.02 0.02 -0.01
vg0103604713 C T 0.01 -0.01 -0.01 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103604713 NA 1.88E-06 mr1210 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
vg0103604713 NA 7.32E-07 mr1278 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
vg0103604713 NA 1.96E-06 mr1305 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
vg0103604713 NA 4.70E-06 mr1319 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
vg0103604713 NA 1.75E-10 mr1322 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
vg0103604713 NA 4.56E-11 mr1332 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
vg0103604713 NA 4.66E-07 mr1358 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
vg0103604713 NA 1.25E-06 mr1374 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
vg0103604713 NA 1.73E-06 mr1379 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
vg0103604713 1.59E-06 1.59E-06 mr1409 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
vg0103604713 2.11E-06 2.11E-06 mr1456 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
vg0103604713 NA 1.07E-06 mr1515 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
vg0103604713 3.65E-06 3.65E-06 mr1516 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
vg0103604713 NA 2.28E-07 mr1527 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
vg0103604713 NA 1.36E-08 mr1585 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
vg0103604713 NA 6.56E-06 mr1586 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
vg0103604713 NA 1.21E-07 mr1659 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
vg0103604713 NA 3.36E-06 mr1836 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
vg0103604713 4.14E-09 4.14E-09 mr1967 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
vg0103604713 NA 7.50E-09 mr1170_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