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Detailed information for vg0321218309:

Variant ID: vg0321218309 (JBrowse)Variation Type: INDEL
Chromosome: chr03Position: 21218309
Reference Allele: AAlternative Allele: ACCTTCCTGGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG,ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG,AC,AGGGAAGTTCCCCCG
Primary Allele: ACCTTCCTGGACTCCCTCTA TAAGCCGGGGAAGTTCCCCC GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGGCGCCATCCTTCGCCTCTTAACCACCCCACTCAACTTTGCCCCCTACTGTCGGACCTGCCCACCACCCATTGCCAACCCTACCGCTCCAGCGCCGCC[A/ACCTTCCTGGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG,ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG,AC,AGGGAAGTTCCCCCG]
CTTAGCTCTCCTCCCACCCCCACTCTCACCCTGACCCAAACCCCCAAACCCTATCTGGTTAGGTCACCACCATCTCGCTGCATGGAATCGCTGCGACTTG

Reverse complement sequence

CAAGTCGCAGCGATTCCATGCAGCGAGATGGTGGTGACCTAACCAGATAGGGTTTGGGGGTTTGGGTCAGGGTGAGAGTGGGGGTGGGAGGAGAGCTAAG[T/CGGGGGAACTTCCCCGGCTTATAGAGGGAGTCCAGGAAGGT,CGGGGGAACTTCCCCGGCTTATAGAGGGAGTCTAGGAAGGT,GT,CGGGGGAACTTCCCT]
GGCGGCGCTGGAGCGGTAGGGTTGGCAATGGGTGGTGGGCAGGTCCGACAGTAGGGGGCAAAGTTGAGTGGGGTGGTTAAGAGGCGAAGGATGGCGCCGA

Allele Frequencies:

Populations Population SizeFrequency of ACCTTCCTGGACTCCCTCTA TAAGCCGGGGAAGTTCCCCC G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.30% 36.00% 1.06% 0.00% AGGGAAGTTCCCCCG: 0.28%; ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.25%; AC: 0.08%
All Indica  2759 94.70% 2.80% 1.81% 0.00% ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.36%; AGGGAAGTTCCCCCG: 0.14%; AC: 0.14%
All Japonica  1512 1.70% 98.20% 0.00% 0.00% ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.07%
Aus  269 95.20% 1.10% 0.00% 0.00% AGGGAAGTTCCCCCG: 3.35%; ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.37%
Indica I  595 95.00% 2.20% 2.86% 0.00% NA
Indica II  465 94.60% 3.20% 1.94% 0.00% AC: 0.22%
Indica III  913 96.70% 2.20% 0.11% 0.00% ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.55%; AC: 0.33%; AGGGAAGTTCCCCCG: 0.11%
Indica Intermediate  786 92.20% 3.80% 2.93% 0.00% ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.64%; AGGGAAGTTCCCCCG: 0.38%
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 4.20% 95.60% 0.00% 0.00% ACCTTCCTAGACTCCCTCTATAAGCCGGGGAAGTTCCCCCG: 0.20%
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0321218309 A -> ACCTTCCTAGACTCCCTCTATAAGCCGGGG AAGTTCCCCCG LOC_Os03g38210.1 downstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> ACCTTCCTAGACTCCCTCTATAAGCCGGGG AAGTTCCCCCG LOC_Os03g38210-LOC_Os03g38230 intergenic_region ; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> ACCTTCCTGGACTCCCTCTATAAGCCGGGG AAGTTCCCCCG LOC_Os03g38210.1 downstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> ACCTTCCTGGACTCCCTCTATAAGCCGGGG AAGTTCCCCCG LOC_Os03g38210-LOC_Os03g38230 intergenic_region ; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> AC LOC_Os03g38210.1 downstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> AC LOC_Os03g38210-LOC_Os03g38230 intergenic_region ; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> AGGGAAGTTCCCCCG LOC_Os03g38210.1 downstream_gene_variant ; 2509.0bp to feature; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N
vg0321218309 A -> AGGGAAGTTCCCCCG LOC_Os03g38210-LOC_Os03g38230 intergenic_region ; MODIFIER silent_mutation Average:72.813; most accessible tissue: Zhenshan97 young leaf, score: 83.199 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321218309 3.74E-06 NA mr1718 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
vg0321218309 1.42E-06 4.71E-10 mr1718 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
vg0321218309 1.86E-07 2.65E-128 mr1750 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
vg0321218309 NA 4.12E-12 mr1750 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
vg0321218309 NA 2.85E-11 mr1718_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
vg0321218309 8.10E-07 1.55E-159 mr1750_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
vg0321218309 NA 3.02E-18 mr1750_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