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Detailed information for vg0914741739:

Variant ID: vg0914741739 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 14741739
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCAAAGACTGTGGAGATTTGCACCAGACCGAAAACAAGCCATACGAGAAGAGCTCGACAAACTTCTCAAAGCTGGCTTCATCAGAGAAGTACTTTATC[T/C]
AGAGTGGCTAGCCAATCCAGTCATGGTGTGGAAGGCCAACGGAAAATGGAGAATGTGTGTCGACTTCACCGACCTCAACAAGGCGTGCCCCAAGGATCAC

Reverse complement sequence

GTGATCCTTGGGGCACGCCTTGTTGAGGTCGGTGAAGTCGACACACATTCTCCATTTTCCGTTGGCCTTCCACACCATGACTGGATTGGCTAGCCACTCT[A/G]
GATAAAGTACTTCTCTGATGAAGCCAGCTTTGAGAAGTTTGTCGAGCTCTTCTCGTATGGCTTGTTTTCGGTCTGGTGCAAATCTCCACAGTCTTTGCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 39.20% 0.40% 57.45% 2.94% NA
All Indica  2759 6.70% 0.60% 88.15% 4.57% NA
All Japonica  1512 99.50% 0.00% 0.46% 0.00% NA
Aus  269 1.10% 0.40% 94.42% 4.09% NA
Indica I  595 3.00% 0.30% 84.37% 12.27% NA
Indica II  465 6.90% 1.30% 89.03% 2.80% NA
Indica III  913 8.40% 0.10% 90.91% 0.55% NA
Indica Intermediate  786 7.30% 1.00% 87.28% 4.45% NA
Temperate Japonica  767 99.50% 0.00% 0.52% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 74.40% 0.00% 23.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0914741739 T -> DEL LOC_Os09g24740.1 N frameshift_variant Average:33.516; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 N N N N
vg0914741739 T -> C LOC_Os09g24740.1 missense_variant ; p.Leu740Pro; MODERATE nonsynonymous_codon ; L740P Average:33.516; most accessible tissue: Zhenshan97 flag leaf, score: 60.074 benign -0.634 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0914741739 NA 1.44E-07 mr1222 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
vg0914741739 NA 8.49E-30 mr1333 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
vg0914741739 NA 3.81E-28 mr1686 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
vg0914741739 NA 6.97E-19 mr1754 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
vg0914741739 NA 2.66E-07 mr1764 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
vg0914741739 NA 5.07E-07 mr1824 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
vg0914741739 NA 8.13E-15 mr1148_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
vg0914741739 NA 1.26E-14 mr1324_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
vg0914741739 NA 2.93E-14 mr1333_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
vg0914741739 NA 2.88E-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
vg0914741739 2.36E-06 NA mr1438_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
vg0914741739 NA 2.02E-09 mr1506_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
vg0914741739 NA 3.56E-14 mr1575_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