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Detailed information for vg0142380984:

Variant ID: vg0142380984 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 42380984
Reference Allele: CAlternative Allele: CTAGTA,A,T
Primary Allele: CSecondary Allele: CTAGTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACGGTGACCTCAGTGCGGCAATTCAGCATGCGAGATCAGCTGGATGGAAGGTCACAACTGAGCATTCCTTTATTAGTTTGTTACTGTTCTTGCAGCCT[C/CTAGTA,A,T]
CTAGCTGCGGCATTCCGCTAATTTTTGGAGGTTGTTTTTCCTGTTCAGGTTCTGAGGCTGCATATGGATGAGCCCTGGAGCAATGGGGAGCACACCACAT

Reverse complement sequence

ATGTGGTGTGCTCCCCATTGCTCCAGGGCTCATCCATATGCAGCCTCAGAACCTGAACAGGAAAAACAACCTCCAAAAATTAGCGGAATGCCGCAGCTAG[G/TACTAG,T,A]
AGGCTGCAAGAACAGTAACAAACTAATAAAGGAATGCTCAGTTGTGACCTTCCATCCAGCTGATCTCGCATGCTGAATTGCCGCACTGAGGTCACCGTCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of CTAGTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 11.30% 0.00% 0.00% A: 0.02%; T: 0.02%
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 68.70% 31.20% 0.00% 0.00% A: 0.07%; T: 0.07%
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 98.40% 1.60% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 81.00% 19.00% 0.00% 0.00% NA
Tropical Japonica  504 55.60% 44.00% 0.00% 0.00% T: 0.20%; A: 0.20%
Japonica Intermediate  241 57.30% 42.70% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg0142380984 C -> T LOC_Os01g73040.1 intron_variant ; MODIFIER silent_mutation Average:73.299; most accessible tissue: Zhenshan97 root, score: 88.851 N N N N
vg0142380984 C -> A LOC_Os01g73040.1 intron_variant ; MODIFIER silent_mutation Average:73.299; most accessible tissue: Zhenshan97 root, score: 88.851 N N N N
vg0142380984 C -> CTAGTA LOC_Os01g73040.1 intron_variant ; MODIFIER silent_mutation Average:73.299; most accessible tissue: Zhenshan97 root, score: 88.851 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)
vg0142380984 C A 0.03 0.02 0.0 0.01 0.02 0.03
vg0142380984 C CTAGT* 0.13 0.2 0.02 0.19 0.24 0.22
vg0142380984 C T -0.01 -0.01 -0.01 -0.01 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0142380984 6.34E-06 NA mr1019_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
vg0142380984 1.55E-06 NA mr1193_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
vg0142380984 1.16E-06 1.16E-06 mr1193_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
vg0142380984 3.02E-06 NA mr1301_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
vg0142380984 NA 8.45E-07 mr1418_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
vg0142380984 NA 6.97E-07 mr1453_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
vg0142380984 NA 1.60E-06 mr1479_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
vg0142380984 NA 9.15E-06 mr1556_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
vg0142380984 NA 2.17E-06 mr1574_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
vg0142380984 NA 6.96E-07 mr1824_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