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Detailed information for vg1008738737:

Variant ID: vg1008738737 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8738737
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTTGCGTACGATGTCCTTTGTCATAGGATTTGGGACTGCCCCTTTTTATGCCCAGATTCCTCATGATCGTCACGAAGAAAAGTGCCGAGTCAAAGTCACC[C/T]
TAAACAGTAATAGTGAAGATATCCCCTCAGTGATGTTCGAAGCTGGAGGAAGAAACTACATTCATGCATGTCAGGAGGTGGCAAGGATCGCCATAGGAGA

Reverse complement sequence

TCTCCTATGGCGATCCTTGCCACCTCCTGACATGCATGAATGTAGTTTCTTCCTCCAGCTTCGAACATCACTGAGGGGATATCTTCACTATTACTGTTTA[G/A]
GGTGACTTTGACTCGGCACTTTTCTTCGTGACGATCATGAGGAATCTGGGCATAAAAAGGGGCAGTCCCAAATCCTATGACAAAGGACATCGTACGCAAC

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 50.20% 0.10% 7.02% 42.62% NA
All Indica  2759 57.80% 0.20% 3.95% 38.09% NA
All Japonica  1512 46.60% 0.10% 0.86% 52.45% NA
Aus  269 0.40% 0.00% 70.26% 29.37% NA
Indica I  595 61.30% 0.00% 1.51% 37.14% NA
Indica II  465 58.90% 0.40% 0.86% 39.78% NA
Indica III  913 56.80% 0.20% 7.12% 35.82% NA
Indica Intermediate  786 55.50% 0.10% 3.94% 40.46% NA
Temperate Japonica  767 58.10% 0.00% 0.52% 41.33% NA
Tropical Japonica  504 23.60% 0.40% 1.59% 74.40% NA
Japonica Intermediate  241 57.70% 0.00% 0.41% 41.91% NA
VI/Aromatic  96 27.10% 0.00% 14.58% 58.33% NA
Intermediate  90 53.30% 0.00% 7.78% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008738737 C -> T LOC_Os10g17350.1 synonymous_variant ; p.Leu74Leu; LOW synonymous_codon Average:13.306; most accessible tissue: Callus, score: 19.293 N N N N
vg1008738737 C -> DEL LOC_Os10g17350.1 N frameshift_variant Average:13.306; most accessible tissue: Callus, score: 19.293 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008738737 NA 3.56E-07 mr1113 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
vg1008738737 NA 7.51E-06 mr1116 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
vg1008738737 NA 4.95E-12 mr1118 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
vg1008738737 NA 9.98E-10 mr1161 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
vg1008738737 NA 6.61E-25 mr1495 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
vg1008738737 NA 3.47E-14 mr1495 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
vg1008738737 NA 5.57E-06 mr1496 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
vg1008738737 1.13E-06 NA mr1798 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
vg1008738737 NA 3.52E-06 mr1798 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
vg1008738737 NA 1.48E-06 mr1113_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
vg1008738737 NA 5.66E-07 mr1114_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
vg1008738737 NA 3.28E-14 mr1118_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
vg1008738737 NA 3.79E-07 mr1120_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
vg1008738737 NA 2.15E-09 mr1161_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
vg1008738737 NA 3.28E-06 mr1247_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
vg1008738737 NA 3.91E-14 mr1495_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