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Detailed information for vg0604192525:

Variant ID: vg0604192525 (JBrowse)Variation Type: INDEL
Chromosome: chr06Position: 4192525
Reference Allele: TCCGAlternative Allele: T,GCCG,TCCGCCG
Primary Allele: TCCGSecondary Allele: GCCG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCAGGTACTGCATCGCCGTGCCCATGTCCTCCTCCATCATCTTCGCCACCTGCTGCTCCGTCACCCGCATCCCACCACCGGTGCCACCTCCTCCTCCTCC[TCCG/T,GCCG,TCCGCCG]
CCGCCGCCGCCGCCCTCGCCGCCGGTGCCGCCCTTGCTCGCCTTGCCACCGCCGCCATTGCTGCTCCCGTTGCTGTTCCCCTGCACGGACGCACGACGTC

Reverse complement sequence

GACGTCGTGCGTCCGTGCAGGGGAACAGCAACGGGAGCAGCAATGGCGGCGGTGGCAAGGCGAGCAAGGGCGGCACCGGCGGCGAGGGCGGCGGCGGCGG[CGGA/A,CGGC,CGGCGGA]
GGAGGAGGAGGAGGTGGCACCGGTGGTGGGATGCGGGTGACGGAGCAGCAGGTGGCGAAGATGATGGAGGAGGACATGGGCACGGCGATGCAGTACCTGC

Allele Frequencies:

Populations Population SizeFrequency of TCCG(primary allele) Frequency of GCCG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.70% 16.00% 0.06% 0.00% T: 0.13%; TCCGCCG: 0.08%
All Indica  2759 82.40% 17.50% 0.00% 0.00% T: 0.07%; TCCGCCG: 0.07%
All Japonica  1512 99.50% 0.30% 0.07% 0.00% T: 0.13%
Aus  269 2.60% 95.90% 0.74% 0.00% TCCGCCG: 0.74%
Indica I  595 79.80% 20.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.10% 0.00% 0.00% T: 0.43%
Indica III  913 74.90% 24.90% 0.00% 0.00% TCCGCCG: 0.22%
Indica Intermediate  786 83.50% 16.50% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.40% 0.20% 0.00% T: 0.40%
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 0.00% 0.00% T: 2.22%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0604192525 TCCG -> TCCGCCG LOC_Os06g08500.1 inframe_insertion ; p.Gly261dup; MODERATE inframe_variant Average:79.896; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N
vg0604192525 TCCG -> T LOC_Os06g08500.1 disruptive_inframe_deletion ; p.Gly262del; MODERATE inframe_variant Average:79.896; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N
vg0604192525 TCCG -> GCCG LOC_Os06g08500.1 synonymous_variant ; p.Gly262Gly; LOW synonymous_codon Average:79.896; most accessible tissue: Zhenshan97 young leaf, score: 88.878 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604192525 NA 4.21E-06 mr1283 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
vg0604192525 NA 6.60E-06 mr1314 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
vg0604192525 NA 2.58E-06 mr1417 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
vg0604192525 NA 1.15E-06 mr1424 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
vg0604192525 NA 6.33E-07 mr1485 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
vg0604192525 NA 4.70E-06 mr1512 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
vg0604192525 NA 2.69E-06 mr1611 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
vg0604192525 NA 4.35E-06 mr1634 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
vg0604192525 NA 5.85E-06 mr1665 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
vg0604192525 NA 4.05E-06 mr1759 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
vg0604192525 NA 2.16E-06 mr1774 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
vg0604192525 NA 4.26E-06 mr1787 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
vg0604192525 NA 5.04E-06 mr1820 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
vg0604192525 NA 6.96E-07 mr1906 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
vg0604192525 NA 1.38E-13 mr1909 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
vg0604192525 NA 2.64E-07 mr1920 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
vg0604192525 NA 4.99E-11 mr1921 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
vg0604192525 NA 9.52E-11 mr1939 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
vg0604192525 NA 5.49E-06 mr1952 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