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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0224791280:

Variant ID: vg0224791280 (JBrowse)Variation Type: INDEL
Chromosome: chr02Position: 24791280
Reference Allele: CAlternative Allele: T,CCGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTATACCGTTAGATTGTTAGGTCTT
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATGACACATTAATTCCTACATACAGTTTTTTAGATAAGCATATATCTATCTATCTATCTATTATATTATTAAAACAGCCTTGAAAGAAGACACCACGTT[C/T,CCGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTATACCGTTAGATTGTTAGGTCTT]
GCTGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTACACCGTTAGATTGTTAGGTCTATATTTTAACATATGAGATTTAACATA

Reverse complement sequence

TATGTTAAATCTCATATGTTAAAATATAGACCTAACAATCTAACGGTGTAAATAATTCATATTTTCTCCGATTAATATGAGAATTTCTAGCCTCCACAGC[G/A,AAGACCTAACAATCTAACGGTATAAATAATTCATATTTTCTCCGATTAATATGAGAATTTCTAGCCTCCACGG]
AACGTGGTGTCTTCTTTCAAGGCTGTTTTAATAATATAATAGATAGATAGATAGATATATGCTTATCTAAAAAACTGTATGTAGGAATTAATGTGTCATT

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 48.10% 25.00% 7.15% 19.70% CCGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTATACCGTTAGATTGTTAGGTCTT: 0.02%
All Indica  2759 25.40% 36.20% 8.41% 29.90% CCGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTATACCGTTAGATTGTTAGGTCTT: 0.04%
All Japonica  1512 90.00% 9.30% 0.46% 0.26% NA
Aus  269 24.50% 10.40% 32.34% 32.71% NA
Indica I  595 4.40% 42.00% 12.44% 41.18% NA
Indica II  465 19.40% 32.30% 7.53% 40.86% NA
Indica III  913 41.00% 32.70% 6.57% 19.72% NA
Indica Intermediate  786 26.80% 38.30% 8.02% 26.72% CCGTGGAGGCTAGAAATTCTCATATTAATCGGAGAAAATATGAATTATTTATACCGTTAGATTGTTAGGTCTT: 0.13%
Temperate Japonica  767 93.50% 6.10% 0.13% 0.26% NA
Tropical Japonica  504 91.70% 6.70% 1.19% 0.40% NA
Japonica Intermediate  241 75.50% 24.50% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 0.00% 5.21% 2.08% NA
Intermediate  90 64.40% 14.40% 7.78% 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
vg0224791280 C -> T LOC_Os02g40900.1 upstream_gene_variant ; 4715.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> T LOC_Os02g40910.1 upstream_gene_variant ; 1215.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> T LOC_Os02g40920.1 upstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> T LOC_Os02g40910-LOC_Os02g40920 intergenic_region ; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> CCGTGGAGGCTAGAAATTCTCATATTAATC GGAGAAAATATGAATTATTTATACCGTTAG ATTGTTAGGTCTT LOC_Os02g40900.1 upstream_gene_variant ; 4716.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> CCGTGGAGGCTAGAAATTCTCATATTAATC GGAGAAAATATGAATTATTTATACCGTTAG ATTGTTAGGTCTT LOC_Os02g40910.1 upstream_gene_variant ; 1216.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> CCGTGGAGGCTAGAAATTCTCATATTAATC GGAGAAAATATGAATTATTTATACCGTTAG ATTGTTAGGTCTT LOC_Os02g40920.1 upstream_gene_variant ; 3951.0bp to feature; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> CCGTGGAGGCTAGAAATTCTCATATTAATC GGAGAAAATATGAATTATTTATACCGTTAG ATTGTTAGGTCTT LOC_Os02g40910-LOC_Os02g40920 intergenic_region ; MODIFIER silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N
vg0224791280 C -> DEL N N silent_mutation Average:63.978; most accessible tissue: Callus, score: 92.456 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224791280 9.61E-07 NA mr1101 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
vg0224791280 2.12E-06 NA mr1101 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
vg0224791280 6.50E-06 NA 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
vg0224791280 5.86E-06 NA 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
vg0224791280 9.90E-08 NA mr1099_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
vg0224791280 2.18E-06 NA mr1099_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
vg0224791280 2.82E-06 NA 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
vg0224791280 9.28E-07 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
vg0224791280 6.12E-06 NA 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
vg0224791280 7.31E-07 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
vg0224791280 4.30E-08 NA mr1123_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
vg0224791280 3.48E-06 NA mr1150_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
vg0224791280 2.99E-06 NA mr1150_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
vg0224791280 5.50E-07 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
vg0224791280 2.81E-08 NA 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
vg0224791280 NA 1.13E-08 mr1299_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
vg0224791280 NA 1.01E-08 mr1700_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
vg0224791280 NA 2.19E-07 mr1727_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
vg0224791280 NA 6.63E-10 mr1756_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
vg0224791280 NA 7.03E-07 mr1785_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
vg0224791280 NA 1.45E-07 mr1804_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
vg0224791280 5.09E-06 NA 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
vg0224791280 6.65E-06 NA 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