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Detailed information for vg1117961699:

Variant ID: vg1117961699 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17961699
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: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTCCATTCTGGGATCCTAAGGGGTTGCAGCAAACCTGCCGGTCGCTGGTGCTCAGCCTTCACCTTCTGGCATACGTCGCAAAGTGCTACGTATTCTGCTA[C/T]
GTCTCTTTTCATGTTGGGCCACCAGTATCCTTCCTTCAGATCCTGGTACATCTTCGTACTTCCGGGGTGTAGGGAATAGGCAGATTCATGGGCTTCCTTC

Reverse complement sequence

GAAGGAAGCCCATGAATCTGCCTATTCCCTACACCCCGGAAGTACGAAGATGTACCAGGATCTGAAGGAAGGATACTGGTGGCCCAACATGAAAAGAGAC[G/A]
TAGCAGAATACGTAGCACTTTGCGACGTATGCCAGAAGGTGAAGGCTGAGCACCAGCGACCGGCAGGTTTGCTGCAACCCCTTAGGATCCCAGAATGGAA

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 95.40% 3.20% 0.34% 1.08% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 96.80% 0.10% 0.73% 2.38% NA
Aus  269 48.30% 51.30% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.00% 0.00% 0.39% NA
Tropical Japonica  504 95.60% 0.20% 1.19% 2.98% NA
Japonica Intermediate  241 90.00% 0.40% 2.07% 7.47% NA
VI/Aromatic  96 78.10% 3.10% 3.12% 15.62% NA
Intermediate  90 98.90% 0.00% 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
vg1117961699 C -> T LOC_Os11g30850.1 missense_variant ; p.Val18Ile; MODERATE nonsynonymous_codon ; V18I Average:60.941; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 benign -0.019 TOLERATED 1.00
vg1117961699 C -> DEL LOC_Os11g30850.1 N frameshift_variant Average:60.941; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117961699 3.92E-06 1.92E-17 mr1113 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
vg1117961699 1.44E-07 6.74E-21 mr1114 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
vg1117961699 3.67E-06 5.86E-19 mr1117 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
vg1117961699 5.77E-06 3.99E-18 mr1119 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
vg1117961699 2.62E-06 3.30E-22 mr1120 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
vg1117961699 4.74E-06 4.35E-21 mr1247 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
vg1117961699 NA 1.76E-06 mr1262 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
vg1117961699 4.74E-06 NA mr1917 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
vg1117961699 NA 4.79E-21 mr1961 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
vg1117961699 5.05E-07 1.36E-16 mr1113_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
vg1117961699 2.18E-07 NA mr1114_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
vg1117961699 1.27E-07 4.35E-18 mr1117_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
vg1117961699 1.10E-06 8.29E-17 mr1119_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
vg1117961699 1.28E-06 NA mr1120_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
vg1117961699 8.82E-07 1.30E-18 mr1240_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
vg1117961699 8.29E-07 NA mr1247_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
vg1117961699 NA 2.12E-15 mr1961_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