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

Detailed information for vg0713261979:

Variant ID: vg0713261979 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 13261979
Reference Allele: GCAlternative Allele: AC,G
Primary Allele: GCSecondary Allele: AC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGAGCACTTACTCATATTATATCTTTCTGATACTCTGCTAATGTATGATTTCTGAGATAATCCCAGTACTCCTTTAGACCTATCTCGGTGTATTTCAAT[GC/AC,G]
CTAAAACATAAGATGCCTCACCGAGATCCTTCATATCAAAATTAGATGACAAAAATTCTTTAGTCTGATGCAACATATTAATGTCGCTGCTTGCTAACAG

Reverse complement sequence

CTGTTAGCAAGCAGCGACATTAATATGTTGCATCAGACTAAAGAATTTTTGTCATCTAATTTTGATATGAAGGATCTCGGTGAGGCATCTTATGTTTTAG[GC/GT,C]
ATTGAAATACACCGAGATAGGTCTAAAGGAGTACTGGGATTATCTCAGAAATCATACATTAGCAGAGTATCAGAAAGATATAATATGAGTAAGTGCTCTG

Allele Frequencies:

Populations Population SizeFrequency of GC(primary allele) Frequency of AC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.80% 28.90% 6.83% 0.42% G: 0.04%
All Indica  2759 46.20% 46.30% 7.47% 0.00% G: 0.04%
All Japonica  1512 89.70% 2.10% 6.75% 1.32% G: 0.07%
Aus  269 82.90% 14.10% 2.97% 0.00% NA
Indica I  595 78.20% 14.10% 7.73% 0.00% NA
Indica II  465 71.80% 22.40% 5.81% 0.00% NA
Indica III  913 14.10% 79.50% 6.24% 0.00% G: 0.11%
Indica Intermediate  786 44.10% 46.20% 9.67% 0.00% NA
Temperate Japonica  767 93.90% 1.40% 3.91% 0.65% G: 0.13%
Tropical Japonica  504 89.90% 1.00% 8.73% 0.40% NA
Japonica Intermediate  241 76.30% 6.60% 11.62% 5.39% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 72.20% 20.00% 7.78% 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
vg0713261979 GC -> DEL LOC_Os07g23480.1 N frameshift_variant Average:16.256; most accessible tissue: Minghui63 flag leaf, score: 20.769 N N N N
vg0713261979 GC -> AC LOC_Os07g23480.1 synonymous_variant ; p.Gly1770Gly; LOW synonymous_codon Average:16.256; most accessible tissue: Minghui63 flag leaf, score: 20.769 N N N N
vg0713261979 GC -> G LOC_Os07g23480.1 frameshift_variant ; p.Gly1770fs; HIGH frameshift_variant Average:16.256; most accessible tissue: Minghui63 flag leaf, score: 20.769 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0713261979 NA 5.20E-08 mr1063 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
vg0713261979 5.29E-10 3.14E-30 mr1133 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
vg0713261979 1.11E-08 1.94E-22 mr1133 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
vg0713261979 NA 2.23E-07 mr1533 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
vg0713261979 6.32E-06 NA mr1540 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
vg0713261979 1.94E-06 1.94E-06 mr1540 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
vg0713261979 NA 1.25E-06 mr1662 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
vg0713261979 NA 2.68E-08 mr1662 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
vg0713261979 1.70E-07 2.55E-16 mr1667 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
vg0713261979 7.59E-07 1.20E-13 mr1667 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
vg0713261979 7.53E-06 3.75E-06 mr1732 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
vg0713261979 NA 1.34E-06 mr1980 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
vg0713261979 1.27E-11 1.27E-31 mr1133_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
vg0713261979 1.33E-09 4.92E-23 mr1133_2 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
vg0713261979 NA 2.04E-06 mr1662_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
vg0713261979 1.07E-08 6.11E-19 mr1667_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
vg0713261979 9.45E-09 2.43E-16 mr1667_2 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