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Detailed information for vg1117141737:

Variant ID: vg1117141737 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17141737
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CTCTGTACTATGGGCCATGCGTACCACACCGACAACATCCAACAAGGAGACACCCTTCTTCCTCGTGTACGGCTCAGAGGCCATGCTCCCCACTGAGCTA[C/T]
AACATCAGAGTACACGAGTACAGAAGTACTTAGACGAGGACCAGGAGGAGCAGCGAAACGACGACGTGAATCTACTCGAGGAACATCGAGAAAGAGTTGC

Reverse complement sequence

GCAACTCTTTCTCGATGTTCCTCGAGTAGATTCACGTCGTCGTTTCGCTGCTCCTCCTGGTCCTCGTCTAAGTACTTCTGTACTCGTGTACTCTGATGTT[G/A]
TAGCTCAGTGGGGAGCATGGCCTCTGAGCCGTACACGAGGAAGAAGGGTGTCTCCTTGTTGGATGTTGTCGGTGTGGTACGCATGGCCCATAGTACAGAG

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 64.10% 11.20% 11.79% 12.97% NA
All Indica  2759 65.30% 18.60% 14.03% 2.07% NA
All Japonica  1512 59.30% 0.20% 7.34% 33.20% NA
Aus  269 89.20% 0.00% 10.04% 0.74% NA
Indica I  595 84.70% 5.50% 4.87% 4.87% NA
Indica II  465 66.90% 14.40% 18.71% 0.00% NA
Indica III  913 52.20% 30.30% 16.65% 0.77% NA
Indica Intermediate  786 64.80% 17.40% 15.14% 2.67% NA
Temperate Japonica  767 89.80% 0.00% 1.04% 9.13% NA
Tropical Japonica  504 24.60% 0.60% 17.26% 57.54% NA
Japonica Intermediate  241 34.40% 0.00% 6.64% 58.92% NA
VI/Aromatic  96 30.20% 1.00% 22.92% 45.83% NA
Intermediate  90 70.00% 10.00% 11.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117141737 C -> T LOC_Os11g29530.1 stop_gained ; p.Gln1172*; HIGH stop_gained Average:51.654; most accessible tissue: Minghui63 young leaf, score: 74.514 N N N N
vg1117141737 C -> DEL LOC_Os11g29530.1 N frameshift_variant Average:51.654; most accessible tissue: Minghui63 young leaf, score: 74.514 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117141737 NA 4.79E-06 mr1030 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
vg1117141737 NA 9.19E-06 mr1046 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
vg1117141737 NA 3.95E-06 mr1115 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
vg1117141737 NA 9.71E-06 mr1170 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
vg1117141737 NA 7.07E-07 mr1230 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
vg1117141737 9.65E-06 9.65E-06 mr1230 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
vg1117141737 NA 7.16E-06 mr1353 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
vg1117141737 NA 6.29E-06 mr1380 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
vg1117141737 NA 2.74E-07 mr1428 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
vg1117141737 NA 3.69E-07 mr1432 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
vg1117141737 NA 9.80E-07 mr1550 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
vg1117141737 NA 1.15E-06 mr1614 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
vg1117141737 NA 6.49E-06 mr1671 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
vg1117141737 NA 6.68E-06 mr1807 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
vg1117141737 NA 6.34E-06 mr1821 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
vg1117141737 1.25E-06 1.26E-06 mr1869 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
vg1117141737 2.54E-07 2.54E-07 mr1869 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
vg1117141737 NA 3.38E-06 mr1941 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