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

Detailed information for vg0522752497:

Variant ID: vg0522752497 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 22752497
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.05, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


GCTAGCCGTACCACACCGTGAACGGCGCGTGCCAGGCGGCGAAGCTGAACCAGAGCGCGGTCAGCATCGCGGGCTACCGGAACGTGACACCAGCAGCGAG[C/G]
CCGACCTGGCGAGGGCTGTGGCGGCGCAGCCGGTGTTCGTCATCGTCGACGCCGGCAACTTCATGTTCCAGCTCTACGGCAGCGGTGTCTACACGGGGCC

Reverse complement sequence

GGCCCCGTGTAGACACCGCTGCCGTAGAGCTGGAACATGAAGTTGCCGGCGTCGACGATGACGAACACCGGCTGCGCCGCCACAGCCCTCGCCAGGTCGG[G/C]
CTCGCTGCTGGTGTCACGTTCCGGTAGCCCGCGATGCTGACCGCGCTCTGGTTCAGCTTCGCCGCCTGGCACGCGCCGTTCACGGTGTGGTACGGCTAGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.10% 10.30% 5.27% 1.27% NA
All Indica  2759 73.80% 15.90% 8.16% 2.10% NA
All Japonica  1512 96.80% 2.80% 0.26% 0.07% NA
Aus  269 91.80% 0.70% 7.06% 0.37% NA
Indica I  595 55.00% 33.30% 10.42% 1.34% NA
Indica II  465 78.90% 8.60% 9.46% 3.01% NA
Indica III  913 78.80% 13.70% 5.37% 2.19% NA
Indica Intermediate  786 79.30% 9.80% 8.91% 2.04% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 91.50% 8.10% 0.40% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.41% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 4.40% 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
vg0522752497 C -> DEL LOC_Os05g38780.1 N frameshift_variant Average:75.137; most accessible tissue: Minghui63 young leaf, score: 90.17 N N N N
vg0522752497 C -> G LOC_Os05g38780.1 missense_variant ; p.Pro190Ala; MODERATE nonsynonymous_codon ; P190G Average:75.137; most accessible tissue: Minghui63 young leaf, score: 90.17 unknown unknown DELETERIOUS 0.00
vg0522752497 C -> G LOC_Os05g38780.1 missense_variant ; p.Pro190Ala; MODERATE nonsynonymous_codon ; P190A Average:75.137; most accessible tissue: Minghui63 young leaf, score: 90.17 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0522752497 NA 9.84E-06 mr1064 Ind_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
vg0522752497 NA 4.93E-11 mr1195 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
vg0522752497 NA 6.29E-07 mr1195 Ind_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
vg0522752497 NA 3.19E-06 mr1304 Ind_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
vg0522752497 NA 9.34E-06 mr1371 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
vg0522752497 NA 3.05E-06 mr1403 Ind_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
vg0522752497 4.73E-06 4.75E-06 mr1421 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
vg0522752497 1.94E-06 1.94E-06 mr1421 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
vg0522752497 NA 4.77E-06 mr1528 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
vg0522752497 NA 8.71E-06 mr1547 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
vg0522752497 NA 1.77E-07 mr1671 Ind_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
vg0522752497 NA 9.03E-08 mr1716 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
vg0522752497 NA 2.17E-06 mr1735 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
vg0522752497 NA 2.53E-06 mr1735 Ind_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
vg0522752497 NA 4.89E-07 mr1737 Ind_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