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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1205369570:

Variant ID: vg1205369570 (JBrowse)Variation Type: INDEL
Chromosome: chr12Position: 5369570
Reference Allele: TAGTCGGCGGCGGCTTAACCAlternative Allele: CAGTCGGCGGCGGCTTAACC,AAGTCGGCGGCGGCTTAACC,T
Primary Allele: TAGTCGGCGGCGGCTTAACCSecondary Allele: CAGTCGGCGGCGGCTTAACC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATGGTGAAAAGGTTGCATAGCCATGATGAAGTGAACACGAGTCGACGGCAACAGAAGCAAACTGGTAGCGAAGACGCGTAGTTGTGAAGATAAAAACAC[TAGTCGGCGGCGGCTTAACC/CAGTCGGCGGCGGCTTAACC,AAGTCGGCGGCGGCTTAACC,T]
AGTCGGCGACGGAAGAAGTAGAATGATGACGAAAATGAATATGTCCTTGAATGGCAGCAAAATAGGCCAGCCATGAAAGTCAAGGCACCATGGGCGGCGG

Reverse complement sequence

CCGCCGCCCATGGTGCCTTGACTTTCATGGCTGGCCTATTTTGCTGCCATTCAAGGACATATTCATTTTCGTCATCATTCTACTTCTTCCGTCGCCGACT[GGTTAAGCCGCCGCCGACTA/GGTTAAGCCGCCGCCGACTG,GGTTAAGCCGCCGCCGACTT,A]
GTGTTTTTATCTTCACAACTACGCGTCTTCGCTACCAGTTTGCTTCTGTTGCCGTCGACTCGTGTTCACTTCATCATGGCTATGCAACCTTTTCACCATG

Allele Frequencies:

Populations Population SizeFrequency of TAGTCGGCGGCGGCTTAACC(primary allele) Frequency of CAGTCGGCGGCGGCTTAACC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 61.00% 3.20% 4.21% 31.49% AAGTCGGCGGCGGCTTAACC: 0.04%; T: 0.02%
All Indica  2759 41.50% 4.60% 5.69% 48.10% AAGTCGGCGGCGGCTTAACC: 0.07%
All Japonica  1512 96.40% 0.50% 0.40% 2.65% NA
Aus  269 41.30% 5.90% 12.64% 39.78% T: 0.37%
Indica I  595 32.80% 3.90% 5.55% 57.82% NA
Indica II  465 48.60% 3.90% 6.02% 41.08% AAGTCGGCGGCGGCTTAACC: 0.43%
Indica III  913 39.60% 4.70% 5.91% 49.73% NA
Indica Intermediate  786 46.20% 5.50% 5.34% 43.00% NA
Temperate Japonica  767 97.30% 0.40% 0.39% 1.96% NA
Tropical Japonica  504 97.80% 0.60% 0.20% 1.39% NA
Japonica Intermediate  241 90.90% 0.80% 0.83% 7.47% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 83.30% 2.20% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1205369570 TAGTCGGCGGCGGCTTAACC -> DEL N N silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> CAGTCGGCGGCGGCTTAACC LOC_Os12g10150.1 upstream_gene_variant ; 356.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> CAGTCGGCGGCGGCTTAACC LOC_Os12g10140.1 downstream_gene_variant ; 3756.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> CAGTCGGCGGCGGCTTAACC LOC_Os12g10160.1 downstream_gene_variant ; 1706.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> CAGTCGGCGGCGGCTTAACC LOC_Os12g10140-LOC_Os12g10150 intergenic_region ; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> T LOC_Os12g10150.1 upstream_gene_variant ; 355.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> T LOC_Os12g10140.1 downstream_gene_variant ; 3757.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> T LOC_Os12g10160.1 downstream_gene_variant ; 1705.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> T LOC_Os12g10140-LOC_Os12g10150 intergenic_region ; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> AAGTCGGCGGCGGCTTAACC LOC_Os12g10150.1 upstream_gene_variant ; 356.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> AAGTCGGCGGCGGCTTAACC LOC_Os12g10140.1 downstream_gene_variant ; 3756.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> AAGTCGGCGGCGGCTTAACC LOC_Os12g10160.1 downstream_gene_variant ; 1706.0bp to feature; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N
vg1205369570 TAGTCGGCGGCGGCTTAACC -> AAGTCGGCGGCGGCTTAACC LOC_Os12g10140-LOC_Os12g10150 intergenic_region ; MODIFIER silent_mutation Average:11.756; most accessible tissue: Callus, score: 47.115 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1205369570 7.76E-07 NA mr1695_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
vg1205369570 7.21E-06 NA mr1695_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