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Search for Variation information by Variation ID:

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

Detailed information for vg0429705737:

Variant ID: vg0429705737 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 29705737
Reference Allele: ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACGAlternative Allele: A
Primary Allele: ACCGAACAGCGGCGGCATAA TAGGCCAGCCGTGTAGGCGG AGGCACCACTCGGCGGCGAC GGAGGCAAGCCGGCGGTGAA GTCGTAGACGSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGACGTGGACGCCCATGAACGGTGGTGTGACCGACCAACCGTATAGGCGGGGACACCAGTCGGCGGCGACGAAGGCCAGCCGGTCGGCGAAGTCGTAGAC[ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACG/A]
CCCAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCAATCGGCGGCGACGGAGGCAGGCCGGTGGTGAAGTCGTAGACGCCCAACAGCGG

Reverse complement sequence

CCGCTGTTGGGCGTCTACGACTTCACCACCGGCCTGCCTCCGTCGCCGCCGATTGGTGCCTCCGCCTACACGGCTGGCCTATTATGCCGCCGCTGTTGGG[CGTCTACGACTTCACCGCCGGCTTGCCTCCGTCGCCGCCGAGTGGTGCCTCCGCCTACACGGCTGGCCTATTATGCCGCCGCTGTTCGGT/T]
GTCTACGACTTCGCCGACCGGCTGGCCTTCGTCGCCGCCGACTGGTGTCCCCGCCTATACGGTTGGTCGGTCACACCACCGTTCATGGGCGTCCACGTCT

Allele Frequencies:

Populations Population SizeFrequency of ACCGAACAGCGGCGGCATAA TAGGCCAGCCGTGTAGGCGG AGGCACCACTCGGCGGCGAC GGAGGCAAGCCGGCGGTGAA GTCGTAGACG(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.20% 0.00% 1.78% 20.02% NA
All Indica  2759 71.40% 0.10% 2.97% 25.55% NA
All Japonica  1512 85.70% 0.00% 0.07% 14.22% NA
Aus  269 93.70% 0.00% 0.37% 5.95% NA
Indica I  595 55.00% 0.00% 4.37% 40.67% NA
Indica II  465 59.40% 0.00% 1.94% 38.71% NA
Indica III  913 86.40% 0.00% 2.85% 10.73% NA
Indica Intermediate  786 73.50% 0.30% 2.67% 23.54% NA
Temperate Japonica  767 73.10% 0.00% 0.13% 26.73% NA
Tropical Japonica  504 99.20% 0.00% 0.00% 0.79% NA
Japonica Intermediate  241 97.50% 0.00% 0.00% 2.49% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 90.00% 0.00% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0429705737 ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACG -> DEL N N silent_mutation Average:39.792; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0429705737 ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACG -> A LOC_Os04g49830.1 upstream_gene_variant ; 720.0bp to feature; MODIFIER silent_mutation Average:39.792; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0429705737 ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACG -> A LOC_Os04g49840.1 downstream_gene_variant ; 3429.0bp to feature; MODIFIER silent_mutation Average:39.792; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N
vg0429705737 ACCGAACAGCGGCGGCATAATAGGCCAGCCGTGTAGGCGGAGGCACCACTCGGCGGCGACGGAGGCAAGCCGGCGGTGAAGTCGTAGACG -> A LOC_Os04g49830-LOC_Os04g49840 intergenic_region ; MODIFIER silent_mutation Average:39.792; most accessible tissue: Zhenshan97 flag leaf, score: 65.3 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429705737 3.55E-06 3.55E-06 mr1337 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
vg0429705737 8.27E-06 8.27E-06 mr1487 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
vg0429705737 2.04E-08 2.04E-08 mr1572 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
vg0429705737 2.20E-06 2.20E-06 mr1957 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