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Detailed information for vg0822370621:

Variant ID: vg0822370621 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22370621
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGCTGAACAGCTCGGTGACGCAGATCCGCCGCGCCTGGCGCCAGTACGCGCCGTACGGCGACCACGTGATGTCGGCGTAGCCGTAGGTGGTGTGCTTCC[T/C]
GGACGCCGTCCTGGGGCGGTCGATGAACACCGCGTCGTGGGTCTTGAGGACGAGCCTGGCCATGGCGACCGACGAGCCGACGACGACGGGGAAGGAGCCG

Reverse complement sequence

CGGCTCCTTCCCCGTCGTCGTCGGCTCGTCGGTCGCCATGGCCAGGCTCGTCCTCAAGACCCACGACGCGGTGTTCATCGACCGCCCCAGGACGGCGTCC[A/G]
GGAAGCACACCACCTACGGCTACGCCGACATCACGTGGTCGCCGTACGGCGCGTACTGGCGCCAGGCGCGGCGGATCTGCGTCACCGAGCTGTTCAGCGC

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 65.10% 34.60% 0.15% 0.08% NA
All Indica  2759 98.10% 1.60% 0.18% 0.14% NA
All Japonica  1512 1.60% 98.30% 0.07% 0.00% NA
Aus  269 77.70% 22.30% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.34% 0.17% NA
Indica II  465 98.30% 1.30% 0.22% 0.22% NA
Indica III  913 98.80% 1.00% 0.11% 0.11% NA
Indica Intermediate  786 96.20% 3.60% 0.13% 0.13% NA
Temperate Japonica  767 1.60% 98.30% 0.13% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 55.60% 43.30% 1.11% 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
vg0822370621 T -> C LOC_Os08g35510.1 missense_variant ; p.Arg107Gly; MODERATE nonsynonymous_codon ; R107G Average:79.405; most accessible tissue: Minghui63 panicle, score: 87.238 benign -1.4 TOLERATED 1.00
vg0822370621 T -> DEL LOC_Os08g35510.1 N frameshift_variant Average:79.405; most accessible tissue: Minghui63 panicle, score: 87.238 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822370621 NA 2.28E-65 mr1027 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
vg0822370621 NA 8.32E-44 mr1194 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
vg0822370621 NA 1.26E-31 mr1243 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
vg0822370621 NA 6.34E-46 mr1591 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
vg0822370621 NA 1.19E-56 mr1594 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
vg0822370621 NA 1.97E-53 mr1599 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
vg0822370621 NA 6.12E-20 mr1627 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
vg0822370621 NA 7.94E-21 mr1689 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
vg0822370621 NA 3.61E-28 mr1793 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
vg0822370621 NA 1.22E-34 mr1828 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
vg0822370621 NA 2.51E-38 mr1890 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
vg0822370621 NA 9.95E-34 mr1932 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
vg0822370621 NA 5.77E-16 mr1968 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
vg0822370621 NA 8.05E-52 mr1194_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
vg0822370621 NA 4.20E-51 mr1480_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
vg0822370621 NA 1.72E-15 mr1578_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
vg0822370621 NA 1.01E-31 mr1913_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
vg0822370621 NA 2.60E-21 mr1968_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