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Detailed information for vg0111818505:

Variant ID: vg0111818505 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11818505
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAATCGGATGAATCGGCTCACATAGATGTGCGAGGCATGTACAAAAAAATCCTTAAAAATACTTACCTCCGTGCGGAGGGGGAGTCGGCCTAGGAACGTG[C/T]
GCAGCTGGATGGGGACAAGTCGGTACGGGCGGCCGCTGTACAGCTGCGTCTGCCCGAGCAACGTCGTCTGCACGACAGGTGAGCACTCGGAGAATCGAGC

Reverse complement sequence

GCTCGATTCTCCGAGTGCTCACCTGTCGTGCAGACGACGTTGCTCGGGCAGACGCAGCTGTACAGCGGCCGCCCGTACCGACTTGTCCCCATCCAGCTGC[G/A]
CACGTTCCTAGGCCGACTCCCCCTCCGCACGGAGGTAAGTATTTTTAAGGATTTTTTTGTACATGCCTCGCACATCTATGTGAGCCGATTCATCCGATTG

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 83.70% 10.60% 4.70% 1.04% NA
All Indica  2759 91.60% 0.30% 6.60% 1.52% NA
All Japonica  1512 68.40% 31.20% 0.13% 0.33% NA
Aus  269 86.60% 0.00% 13.38% 0.00% NA
Indica I  595 90.80% 0.20% 7.73% 1.34% NA
Indica II  465 97.20% 0.00% 1.72% 1.08% NA
Indica III  913 92.70% 0.20% 5.59% 1.53% NA
Indica Intermediate  786 87.70% 0.60% 9.80% 1.91% NA
Temperate Japonica  767 72.80% 26.60% 0.13% 0.52% NA
Tropical Japonica  504 57.70% 41.90% 0.20% 0.20% NA
Japonica Intermediate  241 76.80% 23.20% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 87.80% 7.80% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0111818505 C -> T LOC_Os01g21190.1 missense_variant ; p.Arg1021His; MODERATE nonsynonymous_codon ; R1021H Average:51.477; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 possibly damaging 1.872 DELETERIOUS 0.03
vg0111818505 C -> DEL LOC_Os01g21190.1 N frameshift_variant Average:51.477; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111818505 NA 1.97E-07 mr1245 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
vg0111818505 NA 2.96E-06 mr1373 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
vg0111818505 3.73E-06 7.90E-07 mr1470 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
vg0111818505 NA 9.89E-08 mr1797 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
vg0111818505 NA 9.89E-08 mr1801 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
vg0111818505 NA 6.32E-06 mr1906 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
vg0111818505 NA 1.75E-06 mr1164_2 Jap_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
vg0111818505 1.56E-07 NA mr1400_2 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
vg0111818505 6.35E-07 6.35E-07 mr1400_2 Jap_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
vg0111818505 NA 4.34E-08 mr1668_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
vg0111818505 NA 6.44E-10 mr1709_2 Jap_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
vg0111818505 NA 5.35E-06 mr1715_2 Jap_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