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Detailed information for vg0315672405:

Variant ID: vg0315672405 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 15672405
Reference Allele: TAlternative Allele: TTCCAATTAGGAAGTACACAGAGACC,TTCCAATTAGGAAGTACACAGAGACG
Primary Allele: TTCCAATTAGGAAGTACACA GAGACCSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AAACAGGTCGTGCTAATTCCATGTTCTTTTCAAAACTGCAGAACAGCTTGTGCTTAATTAGTTATCTTGACTTGTTTAGTTGTTACTCCATTTGCTGTAC[T/TTCCAATTAGGAAGTACACAGAGACC,TTCCAATTAGGAAGTACACAGAGACG]
TCCAATCAGGAAGAGAAAAAAATTATAAAAATACAATGCAGGTTCATCTGATAAACGAGCTCACCTCTTCAAGGAGTAAACTAGTCCCAGCTATCATATG

Reverse complement sequence

CATATGATAGCTGGGACTAGTTTACTCCTTGAAGAGGTGAGCTCGTTTATCAGATGAACCTGCATTGTATTTTTATAATTTTTTTCTCTTCCTGATTGGA[A/GGTCTCTGTGTACTTCCTAATTGGAA,CGTCTCTGTGTACTTCCTAATTGGAA]
GTACAGCAAATGGAGTAACAACTAAACAAGTCAAGATAACTAATTAAGCACAAGCTGTTCTGCAGTTTTGAAAAGAACATGGAATTAGCACGACCTGTTT

Allele Frequencies:

Populations Population SizeFrequency of TTCCAATTAGGAAGTACACA GAGACC(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.90% 35.70% 0.34% 0.00% TTCCAATTAGGAAGTACACAGAGACG: 0.06%
All Indica  2759 89.70% 9.90% 0.36% 0.00% TTCCAATTAGGAAGTACACAGAGACG: 0.11%
All Japonica  1512 23.80% 75.90% 0.26% 0.00% NA
Aus  269 41.60% 58.40% 0.00% 0.00% NA
Indica I  595 91.30% 8.20% 0.50% 0.00% NA
Indica II  465 93.30% 6.20% 0.43% 0.00% NA
Indica III  913 90.10% 9.40% 0.11% 0.00% TTCCAATTAGGAAGTACACAGAGACG: 0.33%
Indica Intermediate  786 85.80% 13.70% 0.51% 0.00% NA
Temperate Japonica  767 3.80% 96.10% 0.13% 0.00% NA
Tropical Japonica  504 54.20% 45.40% 0.40% 0.00% NA
Japonica Intermediate  241 24.10% 75.50% 0.41% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 60.00% 37.80% 2.22% 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
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACC LOC_Os03g27370.1 upstream_gene_variant ; 1314.0bp to feature; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 N N N N
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACC LOC_Os03g27360.1 downstream_gene_variant ; 2928.0bp to feature; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 N N N N
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACC LOC_Os03g27360-LOC_Os03g27370 intergenic_region ; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 N N N N
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACG LOC_Os03g27370.1 upstream_gene_variant ; 1314.0bp to feature; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 N N N N
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACG LOC_Os03g27360.1 downstream_gene_variant ; 2928.0bp to feature; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 N N N N
vg0315672405 T -> TTCCAATTAGGAAGTACACAGAGACG LOC_Os03g27360-LOC_Os03g27370 intergenic_region ; MODIFIER silent_mutation Average:83.134; most accessible tissue: Zhenshan97 root, score: 98.938 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)
vg0315672405 T TTCCA* 0.09 -0.12 -0.12 0.06 0.07 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315672405 3.48E-06 NA mr1036 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
vg0315672405 9.40E-07 1.51E-06 mr1330 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