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

Detailed information for vg0724481626:

Variant ID: vg0724481626 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 24481626
Reference Allele: GAlternative Allele: GGCAGTTCAGGCACCTTCGGCAGCTCCGGCACTTCC
Primary Allele: GSecondary Allele: GGCAGTTCAGGCACCTTCGG CAGCTCCGGCACTTCC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGCAGCTCGACCTTGGGCAACGATGGCAGCTCAGGCTTCGGGAGCTCCGGCACCGCAGGGTGCTCAGGCAATTCAGGCTTCGGCAATTCCGGCACCTC[G/GGCAGTTCAGGCACCTTCGGCAGCTCCGGCACTTCC]
GGGTGTGGCAGTTCAGGCACCTTCGGAAACTCCGGCACGGCGGCGCCATGCGGCAGCTCGGGCTTTGGCAGCTCCGGCACGGCGAGGTGCGGCGGCAGCT

Reverse complement sequence

AGCTGCCGCCGCACCTCGCCGTGCCGGAGCTGCCAAAGCCCGAGCTGCCGCATGGCGCCGCCGTGCCGGAGTTTCCGAAGGTGCCTGAACTGCCACACCC[C/GGAAGTGCCGGAGCTGCCGAAGGTGCCTGAACTGCC]
GAGGTGCCGGAATTGCCGAAGCCTGAATTGCCTGAGCACCCTGCGGTGCCGGAGCTCCCGAAGCCTGAGCTGCCATCGTTGCCCAAGGTCGAGCTGCCGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GGCAGTTCAGGCACCTTCGG CAGCTCCGGCACTTCC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 1.00% 1.08% 0.00% NA
All Indica  2759 99.60% 0.30% 0.14% 0.00% NA
All Japonica  1512 95.60% 1.80% 2.58% 0.00% NA
Aus  269 97.40% 1.90% 0.74% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.10% 0.20% 0.65% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.60% 0.13% 0.00% NA
Temperate Japonica  767 95.80% 0.10% 4.04% 0.00% NA
Tropical Japonica  504 95.40% 4.20% 0.40% 0.00% NA
Japonica Intermediate  241 95.40% 2.10% 2.49% 0.00% NA
VI/Aromatic  96 90.60% 5.20% 4.17% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0724481626 G -> GGCAGTTCAGGCACCTTCGGCAGCTCCGGC ACTTCC LOC_Os07g40890.1 frameshift_variant ; p.Pro89fs; HIGH frameshift_variant Average:75.352; most accessible tissue: Minghui63 panicle, score: 82.797 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724481626 NA 1.68E-09 mr1047 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
vg0724481626 2.84E-08 NA mr1343 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
vg0724481626 5.85E-06 5.86E-06 mr1343 Jap_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
vg0724481626 6.55E-17 NA mr1354 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
vg0724481626 7.74E-14 5.70E-09 mr1354 Jap_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
vg0724481626 NA 1.67E-18 mr1552 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
vg0724481626 NA 6.79E-11 mr1648 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
vg0724481626 3.75E-11 NA mr1829 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
vg0724481626 6.19E-12 6.38E-06 mr1829 Jap_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
vg0724481626 4.26E-07 NA mr1902 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
vg0724481626 5.02E-08 NA mr1902 Jap_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
vg0724481626 NA 6.19E-13 mr1047_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
vg0724481626 NA 1.27E-15 mr1189_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
vg0724481626 3.93E-26 NA mr1354_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
vg0724481626 9.27E-24 7.93E-09 mr1354_2 Jap_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
vg0724481626 NA 3.02E-08 mr1449_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
vg0724481626 NA 1.47E-14 mr1552_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
vg0724481626 6.67E-07 NA mr1567_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
vg0724481626 3.83E-06 NA mr1567_2 Jap_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
vg0724481626 3.51E-06 NA mr1679_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
vg0724481626 2.60E-17 NA mr1829_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
vg0724481626 1.61E-14 4.14E-08 mr1829_2 Jap_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
vg0724481626 1.06E-15 NA mr1902_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
vg0724481626 2.09E-13 3.00E-06 mr1902_2 Jap_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