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Detailed information for vg0620279439:

Variant ID: vg0620279439 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20279439
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGGTGTTGACGTGGTATGCCACAAACACGGACGTGACATGGCATCATCTTGACTGACAAATGGGACCGACTTAAAATTCATTTTCCTTTTTTCTTCTTT[C/T]
CTTCTCATTTTTCTCTCTCTTTTTTTCTTTTTTTCTCCTTTCTCTGTGACCCGAGCACCCCGTGCGGCGGTGGCCTACAGTTGTAGATAGAGAAAGGAGT

Reverse complement sequence

ACTCCTTTCTCTATCTACAACTGTAGGCCACCGCCGCACGGGGTGCTCGGGTCACAGAGAAAGGAGAAAAAAAGAAAAAAAGAGAGAGAAAAATGAGAAG[G/A]
AAAGAAGAAAAAAGGAAAATGAATTTTAAGTCGGTCCCATTTGTCAGTCAAGATGATGCCATGTCACGTCCGTGTTTGTGGCATACCACGTCAACACCAC

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 28.00% 18.50% 2.71% 50.85% NA
All Indica  2759 5.80% 21.80% 4.06% 68.36% NA
All Japonica  1512 73.90% 14.60% 0.40% 11.18% NA
Aus  269 3.00% 2.60% 0.74% 93.68% NA
Indica I  595 10.60% 44.40% 4.37% 40.67% NA
Indica II  465 5.80% 27.30% 6.88% 60.00% NA
Indica III  913 1.30% 3.00% 1.64% 94.09% NA
Indica Intermediate  786 7.40% 23.30% 4.96% 64.38% NA
Temperate Japonica  767 83.20% 8.70% 0.39% 7.69% NA
Tropical Japonica  504 79.00% 6.00% 0.40% 14.68% NA
Japonica Intermediate  241 33.60% 51.00% 0.41% 14.94% NA
VI/Aromatic  96 0.00% 35.40% 0.00% 64.58% NA
Intermediate  90 40.00% 13.30% 8.89% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0620279439 C -> T LOC_Os06g34870.1 intron_variant ; MODIFIER silent_mutation Average:9.586; most accessible tissue: Callus, score: 54.626 N N N N
vg0620279439 C -> DEL N N silent_mutation Average:9.586; most accessible tissue: Callus, score: 54.626 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620279439 NA 2.25E-06 mr1076 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
vg0620279439 NA 2.62E-08 mr1082 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
vg0620279439 2.16E-07 1.51E-09 mr1083 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
vg0620279439 1.22E-06 6.30E-09 mr1086 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
vg0620279439 NA 2.66E-08 mr1103 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
vg0620279439 NA 4.21E-06 mr1104 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
vg0620279439 NA 2.71E-06 mr1107 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
vg0620279439 NA 3.84E-07 mr1145 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
vg0620279439 NA 3.37E-07 mr1162 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
vg0620279439 NA 1.06E-07 mr1226 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
vg0620279439 NA 3.83E-07 mr1408 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
vg0620279439 NA 1.67E-07 mr1411 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
vg0620279439 NA 8.45E-06 mr1437 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
vg0620279439 NA 2.67E-08 mr1510 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
vg0620279439 NA 4.61E-07 mr1560 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
vg0620279439 NA 7.60E-12 mr1938 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