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Detailed information for vg0412260112:

Variant ID: vg0412260112 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 12260112
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.03, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTCCTTCCTATGTTGTACCACTCTTTTTCGTAAGAACGTTTGTAAACTATGTTTTTTTTCTCAAAAGTCTTCTATGTAAAAAATATACTCCTTGTCTT[G/C]
ATGGGCCCATAAACACCGGTTGACATAGTCAACCACCTCAGTGAAGCTCTGTTGTAAATTAACCTCGTTCACCATGGATGGATCAAGGAACCCAACTTGA

Reverse complement sequence

TCAAGTTGGGTTCCTTGATCCATCCATGGTGAACGAGGTTAATTTACAACAGAGCTTCACTGAGGTGGTTGACTATGTCAACCGGTGTTTATGGGCCCAT[C/G]
AAGACAAGGAGTATATTTTTTACATAGAAGACTTTTGAGAAAAAAAACATAGTTTACAAACGTTCTTACGAAAAAGAGTGGTACAACATAGGAAGGACAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.50% 27.20% 19.11% 3.15% NA
All Indica  2759 42.20% 40.10% 14.50% 3.19% NA
All Japonica  1512 67.10% 0.90% 28.51% 3.44% NA
Aus  269 50.90% 48.70% 0.37% 0.00% NA
Indica I  595 48.60% 24.90% 23.70% 2.86% NA
Indica II  465 41.10% 48.40% 9.46% 1.08% NA
Indica III  913 43.40% 36.10% 15.12% 5.37% NA
Indica Intermediate  786 36.80% 51.30% 9.80% 2.16% NA
Temperate Japonica  767 85.40% 0.40% 13.56% 0.65% NA
Tropical Japonica  504 43.10% 1.00% 49.01% 6.94% NA
Japonica Intermediate  241 59.30% 2.50% 33.20% 4.98% NA
VI/Aromatic  96 30.20% 4.20% 56.25% 9.38% NA
Intermediate  90 46.70% 34.40% 18.89% 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
vg0412260112 G -> C LOC_Os04g21670.1 missense_variant ; p.Gln176Glu; MODERATE nonsynonymous_codon ; Q176E Average:32.789; most accessible tissue: Zhenshan97 flower, score: 45.068 benign 0.215 DELETERIOUS 0.02
vg0412260112 G -> DEL LOC_Os04g21670.1 N frameshift_variant Average:32.789; most accessible tissue: Zhenshan97 flower, score: 45.068 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412260112 NA 9.21E-08 mr1062 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
vg0412260112 NA 3.65E-07 mr1386 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
vg0412260112 NA 2.01E-07 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
vg0412260112 NA 1.89E-06 mr1414 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
vg0412260112 NA 7.33E-06 mr1525 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
vg0412260112 NA 8.43E-09 mr1830 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
vg0412260112 1.55E-07 1.53E-19 mr1846 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
vg0412260112 7.75E-08 2.35E-15 mr1846 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
vg0412260112 NA 7.18E-08 mr1317_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
vg0412260112 NA 1.96E-07 mr1608_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
vg0412260112 NA 5.81E-08 mr1608_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
vg0412260112 NA 1.34E-07 mr1818_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
vg0412260112 NA 6.72E-13 mr1830_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
vg0412260112 NA 1.25E-09 mr1830_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
vg0412260112 NA 3.50E-26 mr1846_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
vg0412260112 NA 4.28E-21 mr1846_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