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Detailed information for vg0409740938:

Variant ID: vg0409740938 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 9740938
Reference Allele: CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATTAlternative Allele: C,TGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT
Primary Allele: CGTAGCAATCTCTCACCACA ATCTAGTCCTCGACCAGTAG ATTSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAAAAATTCATCTTCAAGTGATTGGGATACGCCTACACCTGGACTTCGACCAGTAGATCGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGAT[CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT/C,TGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT]
GTAGCAATCTCTCACCACCTAAAAGTTCATTTCTAGGTGATCGAGATACGCCTACACCTGTTCCTCGACCAGTAGATTGTAGTGATATCTCACCACCTAA

Reverse complement sequence

TTAGGTGGTGAGATATCACTACAATCTACTGGTCGAGGAACAGGTGTAGGCGTATCTCGATCACCTAGAAATGAACTTTTAGGTGGTGAGAGATTGCTAC[AATCTACTGGTCGAGGACTAGATTGTGGTGAGAGATTGCTACG/G,AATCTACTGGTCGAGGACTAGATTGTGGTGAGAGATTGCTACA]
ATCTACTGGTCGAGGACTAGATTGTGGTGAGAGATTGCTACGATCTACTGGTCGAAGTCCAGGTGTAGGCGTATCCCAATCACTTGAAGATGAATTTTTA

Allele Frequencies:

Populations Population SizeFrequency of CGTAGCAATCTCTCACCACA ATCTAGTCCTCGACCAGTAG ATT(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.60% 0.10% 0.02% 2.29% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 92.80% 0.00% 0.07% 7.14% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 94.90% 0.00% 0.00% 5.08% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 71.40% 0.00% 0.41% 28.22% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> C LOC_Os04g17770.1 downstream_gene_variant ; 2837.0bp to feature; MODIFIER silent_mutation Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> C LOC_Os04g17780.1 downstream_gene_variant ; 2044.0bp to feature; MODIFIER silent_mutation Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> C LOC_Os04g17770-LOC_Os04g17780 intergenic_region ; MODIFIER silent_mutation Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> DEL N N silent_mutation Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> TGTAGCAATCTCTCACCACAATCTAGTCCT CGACCAGTAGATT LOC_Os04g17770.1 downstream_gene_variant ; 2836.0bp to feature; MODIFIER N Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> TGTAGCAATCTCTCACCACAATCTAGTCCT CGACCAGTAGATT LOC_Os04g17780.1 downstream_gene_variant ; 2045.0bp to feature; MODIFIER N Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 N N N N
vg0409740938 CGTAGCAATCTCTCACCACAATCTAGTCCTCGACCAGTAGATT -> TGTAGCAATCTCTCACCACAATCTAGTCCT CGACCAGTAGATT LOC_Os04g17770-LOC_Os04g17780 intergenic_region ; MODIFIER N Average:72.172; most accessible tissue: Minghui63 young leaf, score: 88.372 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)
vg0409740938 CGTAG* C -0.03 -0.04 -0.01 -0.03 -0.01 -0.03
vg0409740938 CGTAG* TGTAG* 0.0 0.01 0.01 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0409740938 7.63E-06 7.58E-07 mr1397 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
vg0409740938 NA 9.55E-06 mr1448 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
vg0409740938 NA 1.17E-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
vg0409740938 NA 5.76E-08 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
vg0409740938 NA 2.48E-08 mr1871 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