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Detailed information for vg0617705132:

Variant ID: vg0617705132 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 17705132
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCCCTCACGGCTGTGGCTCTCAGGCGGTCACACAACCTGCCTAGGCCCAGTGCTGGGCCTTGACGCGATGGGCCAACAACAAGGTATTCAAGGTATGGG[C/T]
GAGGTTGCCAGGATTGCAACTGTGGTATGCACCAATCAAACAAAATAGTTGCGGAAAATTTGAGGCAGACCAACCAAATAACTAAAAAAAGCGAGAATGT

Reverse complement sequence

ACATTCTCGCTTTTTTTAGTTATTTGGTTGGTCTGCCTCAAATTTTCCGCAACTATTTTGTTTGATTGGTGCATACCACAGTTGCAATCCTGGCAACCTC[G/A]
CCCATACCTTGAATACCTTGTTGTTGGCCCATCGCGTCAAGGCCCAGCACTGGGCCTAGGCAGGTTGTGTGACCGCCTGAGAGCCACAGCCGTGAGGGGT

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 89.40% 8.40% 0.47% 1.76% NA
All Indica  2759 98.70% 1.10% 0.04% 0.22% NA
All Japonica  1512 75.70% 23.90% 0.00% 0.46% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.20% 2.60% 0.00% 0.22% NA
Indica III  913 98.90% 0.50% 0.11% 0.44% NA
Indica Intermediate  786 98.30% 1.50% 0.00% 0.13% NA
Temperate Japonica  767 98.20% 1.70% 0.00% 0.13% NA
Tropical Japonica  504 40.50% 59.10% 0.00% 0.40% NA
Japonica Intermediate  241 77.60% 20.70% 0.00% 1.66% NA
VI/Aromatic  96 15.60% 0.00% 18.75% 65.62% NA
Intermediate  90 80.00% 8.90% 3.33% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0617705132 C -> T LOC_Os06g30600.1 synonymous_variant ; p.Gly11Gly; LOW synonymous_codon Average:61.899; most accessible tissue: Callus, score: 94.341 N N N N
vg0617705132 C -> DEL LOC_Os06g30600.1 N frameshift_variant Average:61.899; most accessible tissue: Callus, score: 94.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0617705132 6.95E-06 NA mr1076 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
vg0617705132 4.52E-07 NA mr1082 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
vg0617705132 1.01E-08 NA mr1083 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
vg0617705132 2.01E-06 NA mr1226 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
vg0617705132 NA 2.95E-07 mr1229 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
vg0617705132 NA 1.51E-25 mr1301 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
vg0617705132 NA 5.28E-09 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
vg0617705132 NA 8.53E-15 mr1410 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
vg0617705132 2.40E-06 NA mr1411 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
vg0617705132 NA 1.12E-06 mr1518 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
vg0617705132 NA 4.20E-08 mr1723 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
vg0617705132 NA 2.35E-06 mr1942 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
vg0617705132 NA 3.26E-09 mr1993 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
vg0617705132 NA 9.31E-21 mr1301_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
vg0617705132 NA 6.34E-13 mr1769_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