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Detailed information for vg0709326096:

Variant ID: vg0709326096 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9326096
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAGGAGTCTCGTCCTCCGAAGGATCAGTGATGTCTGGCTCTATCTCTGGCTCGGTGTCAGTCCCCTCCGTCTCGGAGTCGACCTGGATCGGAGTCTCCAT[G/A]
CTAGAACCCAGCTACGGTGACGGGGTAGGGATCAGTGGAGTGTGCACAATCTCTGGGGCAGGTGGCTGTGTCACTGTCGTGTCCACCAGGTAAGGTGCTG

Reverse complement sequence

CAGCACCTTACCTGGTGGACACGACAGTGACACAGCCACCTGCCCCAGAGATTGTGCACACTCCACTGATCCCTACCCCGTCACCGTAGCTGGGTTCTAG[C/T]
ATGGAGACTCCGATCCAGGTCGACTCCGAGACGGAGGGGACTGACACCGAGCCAGAGATAGAGCCAGACATCACTGATCCTTCGGAGGACGAGACTCCTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.30% 0.30% 23.30% 11.05% NA
All Indica  2759 46.60% 0.50% 36.97% 15.88% NA
All Japonica  1512 95.40% 0.00% 0.60% 3.97% NA
Aus  269 87.70% 0.00% 9.67% 2.60% NA
Indica I  595 71.30% 0.00% 22.86% 5.88% NA
Indica II  465 43.20% 0.40% 38.06% 18.28% NA
Indica III  913 27.20% 0.80% 46.66% 25.41% NA
Indica Intermediate  786 52.50% 0.80% 35.75% 10.94% NA
Temperate Japonica  767 98.20% 0.00% 0.65% 1.17% NA
Tropical Japonica  504 90.10% 0.00% 0.40% 9.52% NA
Japonica Intermediate  241 97.90% 0.00% 0.83% 1.24% NA
VI/Aromatic  96 64.60% 0.00% 27.08% 8.33% NA
Intermediate  90 66.70% 1.10% 22.22% 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
vg0709326096 G -> DEL LOC_Os07g16000.1 N frameshift_variant Average:63.779; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 N N N N
vg0709326096 G -> A LOC_Os07g16000.1 synonymous_variant ; p.Ser226Ser; LOW synonymous_codon Average:63.779; most accessible tissue: Zhenshan97 flag leaf, score: 82.703 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709326096 NA 1.26E-21 mr1003 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
vg0709326096 NA 3.74E-22 mr1051 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
vg0709326096 NA 1.50E-12 mr1326 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
vg0709326096 NA 1.19E-12 mr1362 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
vg0709326096 NA 5.39E-12 mr1744 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
vg0709326096 NA 1.51E-31 mr1051_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
vg0709326096 NA 2.86E-08 mr1335_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