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Detailed information for vg0904668868:

Variant ID: vg0904668868 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4668868
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGATGCTGTGGACCACAATGCTCGAGACGTTCACGCAACCCGTGGGTACGGAGAACATAGTGAAACAGTGGACTCTGAAGAAAATGGCAGAACAGTTC[C/T]
AGAGCTTGAAGGGAGATCTCTACAAGAAATACATCCTGAAGGGACTAACACCGAACTTCGACGTATTCCCAAAGGTAAGGGATCATTGGGATGAGTTCGT

Reverse complement sequence

ACGAACTCATCCCAATGATCCCTTACCTTTGGGAATACGTCGAAGTTCGGTGTTAGTCCCTTCAGGATGTATTTCTTGTAGAGATCTCCCTTCAAGCTCT[G/A]
GAACTGTTCTGCCATTTTCTTCAGAGTCCACTGTTTCACTATGTTCTCCGTACCCACGGGTTGCGTGAACGTCTCGAGCATTGTGGTCCACAGCATCTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.70% 8.80% 12.19% 4.27% NA
All Indica  2759 76.50% 4.40% 13.81% 5.33% NA
All Japonica  1512 69.40% 16.60% 10.91% 3.11% NA
Aus  269 91.80% 6.30% 1.12% 0.74% NA
Indica I  595 74.80% 3.00% 15.29% 6.89% NA
Indica II  465 80.00% 4.50% 12.04% 3.44% NA
Indica III  913 75.70% 5.80% 12.60% 5.91% NA
Indica Intermediate  786 76.60% 3.70% 15.14% 4.58% NA
Temperate Japonica  767 92.60% 0.70% 1.96% 4.82% NA
Tropical Japonica  504 40.10% 37.30% 21.83% 0.79% NA
Japonica Intermediate  241 56.80% 24.10% 16.60% 2.49% NA
VI/Aromatic  96 63.50% 19.80% 14.58% 2.08% NA
Intermediate  90 71.10% 10.00% 14.44% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0904668868 C -> T LOC_Os09g08850.1 N stop_gained Average:27.025; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N
vg0904668868 C -> DEL LOC_Os09g08850.1 N frameshift_variant Average:27.025; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904668868 3.13E-07 4.12E-10 mr1422 Jap_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
vg0904668868 NA 4.77E-09 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
vg0904668868 6.89E-07 NA mr1850_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