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Detailed information for vg1117949081:

Variant ID: vg1117949081 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17949081
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGGGCCGAGAAGAATGAAATGAAAAAGGAGAAAATTGGCTATGAGAATAACTCGCACGAAGATGATATATGAGAATAAAATGGATAAGCATATATACTAT[C/A]
TTTGATGCTAAGCACAAGATGTCTTATATATGAAACCAATCAAATTGATGTGGTTAATATGGTAAAGACTAGAGAGTCCATTAATATACCCCTCGGTTAC

Reverse complement sequence

GTAACCGAGGGGTATATTAATGGACTCTCTAGTCTTTACCATATTAACCACATCAATTTGATTGGTTTCATATATAAGACATCTTGTGCTTAGCATCAAA[G/T]
ATAGTATATATGCTTATCCATTTTATTCTCATATATCATCTTCGTGCGAGTTATTCTCATAGCCAATTTTCTCCTTTTTCATTTCATTCTTCTCGGCCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.40% 7.90% 4.38% 18.28% NA
All Indica  2759 64.90% 0.50% 6.38% 28.27% NA
All Japonica  1512 72.40% 23.20% 0.53% 3.90% NA
Aus  269 89.20% 1.50% 6.32% 2.97% NA
Indica I  595 90.30% 0.00% 1.18% 8.57% NA
Indica II  465 65.20% 0.00% 4.95% 29.89% NA
Indica III  913 48.20% 1.10% 11.50% 39.21% NA
Indica Intermediate  786 64.90% 0.40% 5.22% 29.52% NA
Temperate Japonica  767 97.00% 2.10% 0.00% 0.91% NA
Tropical Japonica  504 48.40% 41.50% 0.99% 9.13% NA
Japonica Intermediate  241 44.00% 52.30% 1.24% 2.49% NA
VI/Aromatic  96 94.80% 0.00% 0.00% 5.21% NA
Intermediate  90 73.30% 6.70% 6.67% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117949081 C -> A LOC_Os11g30820.1 upstream_gene_variant ; 690.0bp to feature; MODIFIER silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1117949081 C -> A LOC_Os11g30830.1 upstream_gene_variant ; 3777.0bp to feature; MODIFIER silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1117949081 C -> A LOC_Os11g30810.1 downstream_gene_variant ; 3691.0bp to feature; MODIFIER silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1117949081 C -> A LOC_Os11g30840.1 downstream_gene_variant ; 4551.0bp to feature; MODIFIER silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1117949081 C -> A LOC_Os11g30820-LOC_Os11g30830 intergenic_region ; MODIFIER silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N
vg1117949081 C -> DEL N N silent_mutation Average:39.753; most accessible tissue: Zhenshan97 panicle, score: 52.263 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117949081 NA 2.20E-06 mr1543 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
vg1117949081 NA 2.91E-06 mr1020_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
vg1117949081 8.76E-08 4.09E-24 mr1042_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
vg1117949081 NA 2.91E-09 mr1042_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
vg1117949081 NA 1.15E-06 mr1043_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
vg1117949081 NA 2.86E-06 mr1043_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
vg1117949081 NA 8.72E-06 mr1091_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
vg1117949081 8.94E-06 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
vg1117949081 6.26E-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
vg1117949081 1.73E-06 NA mr1123_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
vg1117949081 1.10E-06 NA mr1242_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
vg1117949081 NA 1.05E-07 mr1269_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
vg1117949081 9.93E-06 9.91E-06 mr1286_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
vg1117949081 NA 1.44E-06 mr1289_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
vg1117949081 NA 1.46E-06 mr1291_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
vg1117949081 NA 9.53E-06 mr1291_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
vg1117949081 NA 5.36E-07 mr1397_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
vg1117949081 NA 7.24E-07 mr1453_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
vg1117949081 NA 2.23E-09 mr1479_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
vg1117949081 NA 3.00E-06 mr1479_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
vg1117949081 5.68E-06 NA mr1496_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
vg1117949081 2.70E-06 2.30E-13 mr1502_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
vg1117949081 NA 1.83E-09 mr1502_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
vg1117949081 2.01E-06 4.56E-14 mr1543_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
vg1117949081 NA 7.99E-10 mr1543_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
vg1117949081 NA 2.05E-06 mr1556_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
vg1117949081 NA 1.43E-06 mr1621_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
vg1117949081 NA 3.81E-06 mr1621_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
vg1117949081 NA 1.01E-06 mr1665_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
vg1117949081 NA 1.90E-06 mr1677_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
vg1117949081 6.57E-09 1.41E-17 mr1680_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
vg1117949081 NA 2.45E-09 mr1680_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
vg1117949081 NA 3.99E-07 mr1687_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
vg1117949081 NA 8.26E-06 mr1722_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
vg1117949081 NA 4.84E-06 mr1738_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
vg1117949081 5.10E-07 5.70E-18 mr1742_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
vg1117949081 NA 3.62E-09 mr1742_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
vg1117949081 NA 2.16E-06 mr1764_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
vg1117949081 7.19E-08 2.96E-26 mr1871_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
vg1117949081 NA 1.95E-09 mr1871_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
vg1117949081 NA 1.48E-06 mr1892_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
vg1117949081 NA 9.16E-06 mr1929_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
vg1117949081 NA 4.05E-07 mr1966_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