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Detailed information for vg0611421749:

Variant ID: vg0611421749 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11421749
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAACAAACTTTTTTAAGTAGTGCTAACACAAATACGGTGTTTGGCTTAGGAATGATAAACGCATACACGAAAGTTATTTTGTGGCACTGCACACTGGTG[G/C]
AGGTTTTTCTTTTCCCTCGCGGTACTTTTTACTTTACTTGGCCACACCTCCACCAACATGTGAGGTCCTTAAGTGATCCGCATACAAAAATATCTCCTCT

Reverse complement sequence

AGAGGAGATATTTTTGTATGCGGATCACTTAAGGACCTCACATGTTGGTGGAGGTGTGGCCAAGTAAAGTAAAAAGTACCGCGAGGGAAAAGAAAAACCT[C/G]
CACCAGTGTGCAGTGCCACAAAATAACTTTCGTGTATGCGTTTATCATTCCTAAGCCAAACACCGTATTTGTGTTAGCACTACTTAAAAAAGTTTGTTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.10% 38.40% 0.17% 6.39% NA
All Indica  2759 86.00% 5.40% 0.25% 8.34% NA
All Japonica  1512 7.10% 88.50% 0.00% 4.37% NA
Aus  269 26.00% 74.00% 0.00% 0.00% NA
Indica I  595 89.10% 9.10% 0.17% 1.68% NA
Indica II  465 95.10% 2.80% 0.43% 1.72% NA
Indica III  913 84.30% 1.80% 0.11% 13.80% NA
Indica Intermediate  786 80.30% 8.40% 0.38% 10.94% NA
Temperate Japonica  767 3.90% 96.00% 0.00% 0.13% NA
Tropical Japonica  504 12.50% 75.20% 0.00% 12.30% NA
Japonica Intermediate  241 6.20% 92.50% 0.00% 1.24% NA
VI/Aromatic  96 14.60% 84.40% 0.00% 1.04% NA
Intermediate  90 42.20% 51.10% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611421749 G -> C LOC_Os06g19950.1 upstream_gene_variant ; 1861.0bp to feature; MODIFIER silent_mutation Average:63.889; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0611421749 G -> C LOC_Os06g19940.1 intron_variant ; MODIFIER silent_mutation Average:63.889; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg0611421749 G -> DEL N N silent_mutation Average:63.889; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611421749 NA 8.96E-59 mr1065 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
vg0611421749 NA 5.09E-55 mr1068 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
vg0611421749 NA 4.56E-57 mr1087 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
vg0611421749 NA 5.19E-55 mr1090 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
vg0611421749 NA 8.04E-47 mr1111 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
vg0611421749 NA 9.87E-48 mr1121 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
vg0611421749 NA 8.03E-44 mr1144 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
vg0611421749 1.61E-07 NA mr1148 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
vg0611421749 NA 1.08E-09 mr1151 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
vg0611421749 NA 1.04E-44 mr1200 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
vg0611421749 NA 3.21E-51 mr1211 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
vg0611421749 NA 8.25E-30 mr1237 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
vg0611421749 NA 3.75E-09 mr1249 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
vg0611421749 NA 2.01E-14 mr1261 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
vg0611421749 NA 2.52E-62 mr1065_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
vg0611421749 NA 1.41E-67 mr1068_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
vg0611421749 NA 6.72E-09 mr1068_2 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
vg0611421749 NA 4.43E-62 mr1090_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
vg0611421749 NA 2.33E-53 mr1111_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
vg0611421749 NA 4.83E-09 mr1111_2 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
vg0611421749 NA 2.40E-08 mr1112_2 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
vg0611421749 NA 1.79E-51 mr1144_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
vg0611421749 NA 1.40E-06 mr1144_2 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
vg0611421749 7.41E-08 3.17E-10 mr1165_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
vg0611421749 NA 1.29E-55 mr1200_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
vg0611421749 NA 4.24E-08 mr1200_2 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
vg0611421749 NA 5.02E-59 mr1211_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
vg0611421749 NA 6.74E-06 mr1341_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
vg0611421749 NA 5.57E-58 mr1526_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
vg0611421749 NA 3.57E-08 mr1526_2 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
vg0611421749 5.61E-08 5.61E-08 mr1971_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