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Detailed information for vg0818186893:

Variant ID: vg0818186893 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 18186893
Reference Allele: CCAAlternative Allele: TCA,C
Primary Allele: CCASecondary Allele: TCA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTAAAATGTAATAAGTTCATAATACTCCATCCATCTACTTTTGATAGTCATATTTCATCTTGGCACACAGACCAACGATAAGTGATTCTACTTATCAT[CCA/TCA,C]
TTTAAACATGCTTCCATTTAAACATGCTACTAGTCATTCCTCGTGAACAAGCGATTCATTAATATTTACATTTCTCGATGCCCATGTAGCCAATCTTGTG

Reverse complement sequence

CACAAGATTGGCTACATGGGCATCGAGAAATGTAAATATTAATGAATCGCTTGTTCACGAGGAATGACTAGTAGCATGTTTAAATGGAAGCATGTTTAAA[TGG/TGA,G]
ATGATAAGTAGAATCACTTATCGTTGGTCTGTGTGCCAAGATGAAATATGACTATCAAAAGTAGATGGATGGAGTATTATGAACTTATTACATTTTAGAG

Allele Frequencies:

Populations Population SizeFrequency of CCA(primary allele) Frequency of TCA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.50% 1.50% 2.18% 17.69% C: 0.13%
All Indica  2759 70.40% 0.60% 1.88% 27.04% C: 0.11%
All Japonica  1512 95.80% 0.00% 0.20% 3.90% C: 0.13%
Aus  269 58.40% 19.00% 15.99% 6.69% NA
Indica I  595 61.50% 0.00% 1.18% 36.81% C: 0.50%
Indica II  465 24.70% 0.20% 2.15% 72.90% NA
Indica III  913 97.90% 0.70% 1.31% 0.11% NA
Indica Intermediate  786 72.10% 1.10% 2.93% 23.79% NA
Temperate Japonica  767 98.60% 0.00% 0.13% 1.04% C: 0.26%
Tropical Japonica  504 93.50% 0.00% 0.20% 6.35% NA
Japonica Intermediate  241 91.70% 0.00% 0.41% 7.88% NA
VI/Aromatic  96 97.90% 1.00% 1.04% 0.00% NA
Intermediate  90 78.90% 1.10% 4.44% 14.44% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818186893 CCA -> C LOC_Os08g29650.1 upstream_gene_variant ; 2512.0bp to feature; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> C LOC_Os08g29640.1 downstream_gene_variant ; 1416.0bp to feature; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> C LOC_Os08g29640-LOC_Os08g29650 intergenic_region ; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> DEL N N silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> TCA LOC_Os08g29650.1 upstream_gene_variant ; 2513.0bp to feature; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> TCA LOC_Os08g29640.1 downstream_gene_variant ; 1415.0bp to feature; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N
vg0818186893 CCA -> TCA LOC_Os08g29640-LOC_Os08g29650 intergenic_region ; MODIFIER silent_mutation Average:25.2; most accessible tissue: Zhenshan97 flower, score: 42.409 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818186893 NA 3.40E-07 mr1028 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
vg0818186893 NA 5.54E-24 mr1095 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
vg0818186893 NA 4.55E-37 mr1098 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
vg0818186893 NA 3.61E-30 mr1099 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
vg0818186893 NA 1.83E-30 mr1101 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
vg0818186893 NA 1.49E-20 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
vg0818186893 NA 2.21E-22 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
vg0818186893 7.42E-06 8.60E-20 mr1116 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
vg0818186893 6.32E-07 1.11E-26 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
vg0818186893 NA 1.73E-22 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
vg0818186893 NA 3.22E-26 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
vg0818186893 2.46E-07 3.45E-33 mr1123 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
vg0818186893 NA 1.65E-06 mr1126 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
vg0818186893 NA 1.99E-06 mr1184 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
vg0818186893 NA 9.54E-23 mr1240 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
vg0818186893 NA 1.20E-21 mr1242 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
vg0818186893 NA 4.20E-28 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
vg0818186893 NA 4.37E-08 mr1348 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
vg0818186893 NA 2.81E-06 mr1349 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
vg0818186893 NA 3.42E-06 mr1365 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
vg0818186893 NA 2.13E-08 mr1369 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
vg0818186893 NA 1.77E-06 mr1445 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
vg0818186893 NA 8.83E-09 mr1453 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
vg0818186893 NA 1.70E-17 mr1496 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
vg0818186893 NA 6.73E-27 mr1589 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
vg0818186893 NA 2.94E-08 mr1652 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
vg0818186893 NA 1.30E-10 mr1696 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
vg0818186893 NA 9.02E-08 mr1706 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
vg0818186893 NA 5.18E-10 mr1730 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
vg0818186893 NA 2.17E-30 mr1858 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
vg0818186893 NA 1.98E-30 mr1859 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
vg0818186893 NA 2.36E-27 mr1868 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
vg0818186893 NA 2.69E-06 mr1906 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
vg0818186893 NA 2.21E-17 mr1911 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
vg0818186893 NA 1.97E-26 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
vg0818186893 NA 1.57E-13 mr1918 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
vg0818186893 NA 8.42E-23 mr1936 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
vg0818186893 NA 1.39E-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
vg0818186893 NA 6.89E-22 mr1095_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
vg0818186893 NA 6.50E-38 mr1098_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
vg0818186893 NA 8.02E-28 mr1099_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
vg0818186893 5.41E-06 3.82E-23 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
vg0818186893 1.27E-06 1.55E-22 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
vg0818186893 2.71E-07 8.52E-26 mr1117_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
vg0818186893 1.11E-06 8.21E-23 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
vg0818186893 3.10E-07 2.43E-31 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
vg0818186893 1.52E-07 3.91E-30 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
vg0818186893 NA 2.00E-23 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
vg0818186893 8.91E-08 1.07E-31 mr1247_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
vg0818186893 NA 4.80E-09 mr1388_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
vg0818186893 NA 4.97E-15 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
vg0818186893 NA 1.10E-30 mr1549_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
vg0818186893 NA 5.19E-08 mr1707_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
vg0818186893 NA 2.58E-15 mr1911_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
vg0818186893 NA 9.87E-14 mr1918_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
vg0818186893 NA 3.61E-06 mr1929_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
vg0818186893 NA 3.53E-19 mr1936_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
vg0818186893 NA 2.84E-19 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