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Detailed information for vg0609889578:

Variant ID: vg0609889578 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9889578
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATAAGCATCATGAACATACCAAGAATGCAATAGAATTGCGACTAACAGGACAAACAGAGGTATCAAAGAATGAGTTAACAGTAGGAGAAAGACATACCC[C/T]
GAGAATGTCCCTCCACTGGATTGTGAGGCAGAATTGCCTCCGTTGACGTTGACGTTCGCAGCGGCTCCGGCTCCCGGCGCGCCATCTTCAGGGATGGCGG

Reverse complement sequence

CCGCCATCCCTGAAGATGGCGCGCCGGGAGCCGGAGCCGCTGCGAACGTCAACGTCAACGGAGGCAATTCTGCCTCACAATCCAGTGGAGGGACATTCTC[G/A]
GGGTATGTCTTTCTCCTACTGTTAACTCATTCTTTGATACCTCTGTTTGTCCTGTTAGTCGCAATTCTATTGCATTCTTGGTATGTTCATGATGCTTATT

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 88.10% 8.10% 0.61% 3.13% NA
All Indica  2759 89.10% 4.90% 0.94% 5.15% NA
All Japonica  1512 84.10% 15.50% 0.13% 0.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 87.60% 10.10% 0.84% 1.51% NA
Indica II  465 91.20% 1.50% 1.29% 6.02% NA
Indica III  913 87.40% 2.10% 1.31% 9.20% NA
Indica Intermediate  786 90.80% 6.10% 0.38% 2.67% NA
Temperate Japonica  767 94.10% 5.60% 0.00% 0.26% NA
Tropical Japonica  504 68.10% 31.20% 0.40% 0.40% NA
Japonica Intermediate  241 85.90% 14.10% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 78.90% 18.90% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0609889578 C -> T LOC_Os06g17050.1 splice_region_variant&synonymous_variant ; p.Ser47Ser; LOW synonymous_codon Average:39.251; most accessible tissue: Minghui63 root, score: 56.226 N N N N
vg0609889578 C -> DEL LOC_Os06g17050.1 N frameshift_variant Average:39.251; most accessible tissue: Minghui63 root, score: 56.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609889578 NA 3.57E-06 mr1087 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
vg0609889578 NA 3.78E-07 mr1090 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
vg0609889578 NA 3.56E-07 mr1094 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
vg0609889578 NA 1.10E-06 mr1111 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
vg0609889578 NA 1.15E-06 mr1121 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
vg0609889578 2.52E-06 NA mr1695 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
vg0609889578 1.21E-13 1.46E-17 mr1695 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
vg0609889578 3.31E-08 NA mr1695_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
vg0609889578 1.71E-15 4.94E-14 mr1695_2 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