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Detailed information for vg1121947567:

Variant ID: vg1121947567 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21947567
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


AAGACAAATATGGTGCTCAAAGATTTTGGTGGTAATCCATCGGAGACCAAAGGTGTTTTAAATGTGGAGCTGACAGTCGGCAGTAAAACTATTCCTACCA[C/T]
GTTTTTTGTCATTGATGGGAAGGGTTCATACAGTTTGTTGCTTGGAAGATATTGGATTCATGCCAATTGTTGCATCCCTTCAACTATGCATCAGTGCTTG

Reverse complement sequence

CAAGCACTGATGCATAGTTGAAGGGATGCAACAATTGGCATGAATCCAATATCTTCCAAGCAACAAACTGTATGAACCCTTCCCATCAATGACAAAAAAC[G/A]
TGGTAGGAATAGTTTTACTGCCGACTGTCAGCTCCACATTTAAAACACCTTTGGTCTCCGATGGATTACCACCAAAATCTTTGAGCACCATATTTGTCTT

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 82.80% 13.60% 0.95% 2.62% NA
All Indica  2759 93.80% 3.10% 0.47% 2.57% NA
All Japonica  1512 70.20% 27.40% 0.73% 1.65% NA
Aus  269 70.30% 16.70% 5.20% 7.81% NA
Indica I  595 99.30% 0.30% 0.00% 0.34% NA
Indica II  465 98.90% 0.60% 0.22% 0.22% NA
Indica III  913 89.40% 5.50% 0.77% 4.38% NA
Indica Intermediate  786 91.90% 3.90% 0.64% 3.56% NA
Temperate Japonica  767 88.40% 11.30% 0.13% 0.13% NA
Tropical Japonica  504 38.90% 55.80% 1.39% 3.97% NA
Japonica Intermediate  241 77.60% 19.50% 1.24% 1.66% NA
VI/Aromatic  96 14.60% 75.00% 6.25% 4.17% NA
Intermediate  90 67.80% 27.80% 1.11% 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
vg1121947567 C -> T LOC_Os11g37170.1 missense_variant ; p.Thr835Met; MODERATE nonsynonymous_codon ; T835M Average:28.984; most accessible tissue: Minghui63 flag leaf, score: 42.036 benign 0.903 DELETERIOUS 0.04
vg1121947567 C -> DEL LOC_Os11g37170.1 N frameshift_variant Average:28.984; most accessible tissue: Minghui63 flag leaf, score: 42.036 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121947567 NA 5.94E-06 mr1029 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
vg1121947567 NA 6.40E-06 mr1045 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
vg1121947567 NA 1.84E-10 mr1070 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
vg1121947567 NA 4.09E-06 mr1189 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
vg1121947567 NA 3.73E-08 mr1442 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
vg1121947567 4.22E-06 1.68E-06 mr1470 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
vg1121947567 7.85E-06 7.83E-06 mr1481 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
vg1121947567 NA 9.00E-09 mr1563 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
vg1121947567 NA 9.55E-06 mr1596 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
vg1121947567 NA 1.50E-06 mr1629 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
vg1121947567 NA 2.63E-08 mr1671 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
vg1121947567 1.24E-06 NA mr1679 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
vg1121947567 NA 2.34E-09 mr1679 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
vg1121947567 NA 6.89E-06 mr1780 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
vg1121947567 6.87E-06 NA mr1982 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
vg1121947567 NA 1.42E-07 mr1982 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
vg1121947567 NA 1.17E-06 mr1990 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
vg1121947567 5.21E-06 5.21E-06 mr1760_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