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Detailed information for vg0100790202:

Variant ID: vg0100790202 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 790202
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCAGAAGCTCGCTTCAACAAATGTATCAACTGCCGTGTACGAACCTCAAAAGAAAGATGGTGCAACCATAGTAGGGTGTTCAAAAGATTCCATAGCAA[C/T]
AAATCAAGATGGTATTGTTGGCCCAAGATCTTGCCTCAACCTAAGTAGTCATGGAAGCCAGTTATGGTATTTGGTGCCTCCTCGAACATACATGTCTGCT

Reverse complement sequence

AGCAGACATGTATGTTCGAGGAGGCACCAAATACCATAACTGGCTTCCATGACTACTTAGGTTGAGGCAAGATCTTGGGCCAACAATACCATCTTGATTT[G/A]
TTGCTATGGAATCTTTTGAACACCCTACTATGGTTGCACCATCTTTCTTTTGAGGTTCGTACACGGCAGTTGATACATTTGTTGAAGCGAGCTTCTGAAG

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 33.10% 22.80% 1.42% 42.64% NA
All Indica  2759 28.00% 21.80% 1.67% 48.53% NA
All Japonica  1512 44.30% 28.70% 0.73% 26.26% NA
Aus  269 31.20% 4.10% 1.12% 63.57% NA
Indica I  595 1.80% 67.20% 0.17% 30.76% NA
Indica II  465 71.80% 4.30% 0.43% 23.44% NA
Indica III  913 15.30% 3.20% 1.75% 79.74% NA
Indica Intermediate  786 36.60% 19.30% 3.44% 40.59% NA
Temperate Japonica  767 68.60% 2.00% 0.65% 28.81% NA
Tropical Japonica  504 5.80% 77.20% 0.79% 16.27% NA
Japonica Intermediate  241 47.70% 12.40% 0.83% 39.00% NA
VI/Aromatic  96 4.20% 6.20% 4.17% 85.42% NA
Intermediate  90 37.80% 30.00% 3.33% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0100790202 C -> T LOC_Os01g02440.1 missense_variant ; p.Thr79Ile; MODERATE nonsynonymous_codon ; T79I Average:61.044; most accessible tissue: Callus, score: 84.173 unknown unknown TOLERATED 0.25
vg0100790202 C -> DEL LOC_Os01g02440.1 N frameshift_variant Average:61.044; most accessible tissue: Callus, score: 84.173 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100790202 NA 5.29E-09 mr1059 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
vg0100790202 NA 3.00E-11 mr1143 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
vg0100790202 NA 7.20E-10 mr1167 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
vg0100790202 NA 9.56E-10 mr1535 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
vg0100790202 NA 5.73E-09 mr1593 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
vg0100790202 NA 8.38E-10 mr1675 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
vg0100790202 NA 2.11E-07 mr1726 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
vg0100790202 NA 5.80E-08 mr1739 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
vg0100790202 NA 3.48E-08 mr1739 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
vg0100790202 NA 6.29E-07 mr1950 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
vg0100790202 NA 6.70E-10 mr1969 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
vg0100790202 NA 1.39E-11 mr1995 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
vg0100790202 NA 3.39E-06 mr1158_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
vg0100790202 NA 8.58E-09 mr1167_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
vg0100790202 NA 8.52E-06 mr1360_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
vg0100790202 NA 1.57E-06 mr1378_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
vg0100790202 NA 5.23E-08 mr1383_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
vg0100790202 NA 2.72E-07 mr1458_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
vg0100790202 NA 1.68E-10 mr1593_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
vg0100790202 NA 3.00E-06 mr1726_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
vg0100790202 NA 5.11E-10 mr1739_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
vg0100790202 NA 5.91E-11 mr1794_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