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Detailed information for vg0318942572:

Variant ID: vg0318942572 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 18942572
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGGGCACAACTTCATGTATATTGTGCAGACTGTAAAAAGTAAGATAAACCATGTAGCACTTCCCCACTATGAGCCCATGCTTCATGGTGGCAGAGCCGA[C/T]
CTTAGTGGCATCAAGGGCCCATATGGGTGATGTCCATAAAACAAAGGACATCCAAAACGACACTTCAGGGTCGTGCAGAAGGTTCGTTTGCCTCCGATAT

Reverse complement sequence

ATATCGGAGGCAAACGAACCTTCTGCACGACCCTGAAGTGTCGTTTTGGATGTCCTTTGTTTTATGGACATCACCCATATGGGCCCTTGATGCCACTAAG[G/A]
TCGGCTCTGCCACCATGAAGCATGGGCTCATAGTGGGGAAGTGCTACATGGTTTATCTTACTTTTTACAGTCTGCACAATATACATGAAGTTGTGCCCAT

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 86.00% 9.20% 4.32% 0.51% NA
All Indica  2759 77.30% 15.40% 7.21% 0.11% NA
All Japonica  1512 98.50% 0.30% 0.07% 1.19% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 75.00% 8.10% 16.97% 0.00% NA
Indica II  465 94.00% 1.30% 4.73% 0.00% NA
Indica III  913 70.50% 27.90% 1.53% 0.00% NA
Indica Intermediate  786 77.00% 14.80% 7.89% 0.38% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 0.40% 0.00% 7.47% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 90.00% 6.70% 3.33% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0318942572 C -> T LOC_Os03g33100.1 N splice_donor_variant Average:45.889; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg0318942572 C -> DEL LOC_Os03g33100.1 N splice_donor_variant Average:45.889; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0318942572 NA 1.95E-08 mr1221 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
vg0318942572 4.26E-06 NA mr1314 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
vg0318942572 NA 2.46E-09 mr1739 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
vg0318942572 NA 3.18E-07 mr1739 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
vg0318942572 NA 2.73E-06 mr1043_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
vg0318942572 NA 1.81E-06 mr1043_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
vg0318942572 NA 7.07E-06 mr1269_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
vg0318942572 NA 7.46E-06 mr1269_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
vg0318942572 NA 8.94E-06 mr1677_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
vg0318942572 3.43E-06 3.43E-06 mr1912_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