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Search for Variation information by Variation ID:

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

Detailed information for vg0322563907:

Variant ID: vg0322563907 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22563907
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCCTTGCCTGTCGAAAACGCAATTAGCGCCTTCGCCCCATCCAACTCCTTTCGATGAAGGGGGGAGCTATTCGACTCCACCCCGGTCTCATTGTGAC[C/T]
CGGGCTTGGAGTAGGAGTATAGCCAGGGGTGTCGACGCGGTTTTCGACCGCCTCGTCCGCGGCCTTTTCGACCACGACCTCAACCTCCTCCTCTTCCTCC

Reverse complement sequence

GGAGGAAGAGGAGGAGGTTGAGGTCGTGGTCGAAAAGGCCGCGGACGAGGCGGTCGAAAACCGCGTCGACACCCCTGGCTATACTCCTACTCCAAGCCCG[G/A]
GTCACAATGAGACCGGGGTGGAGTCGAATAGCTCCCCCCTTCATCGAAAGGAGTTGGATGGGGCGAAGGCGCTAATTGCGTTTTCGACAGGCAAGGCGGC

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 74.10% 5.50% 12.08% 8.34% NA
All Indica  2759 58.20% 7.90% 19.79% 14.10% NA
All Japonica  1512 99.70% 0.20% 0.00% 0.07% NA
Aus  269 79.20% 12.60% 7.81% 0.37% NA
Indica I  595 52.10% 6.40% 27.73% 13.78% NA
Indica II  465 80.60% 3.90% 10.54% 4.95% NA
Indica III  913 49.80% 9.90% 20.81% 19.50% NA
Indica Intermediate  786 59.30% 9.20% 18.07% 13.49% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 5.60% 4.44% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0322563907 C -> T LOC_Os03g40580.1 missense_variant ; p.Gly241Ser; MODERATE nonsynonymous_codon ; G241S Average:47.144; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 possibly damaging 1.603 TOLERATED 0.06
vg0322563907 C -> DEL LOC_Os03g40580.1 N frameshift_variant Average:47.144; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322563907 NA 8.94E-07 mr1204_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
vg0322563907 NA 4.83E-06 mr1204_2 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
vg0322563907 NA 4.74E-07 mr1252_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
vg0322563907 NA 1.22E-06 mr1406_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
vg0322563907 NA 4.45E-07 mr1408_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
vg0322563907 NA 1.24E-06 mr1554_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
vg0322563907 9.24E-06 9.22E-06 mr1605_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
vg0322563907 NA 3.83E-08 mr1837_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
vg0322563907 NA 1.82E-06 mr1876_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
vg0322563907 NA 6.50E-09 mr1947_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
vg0322563907 4.82E-06 4.82E-06 mr1947_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
vg0322563907 5.71E-06 5.69E-06 mr1953_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