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Detailed information for vg1218883751:

Variant ID: vg1218883751 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18883751
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTCCAACCATGTCACTCATGGGTTAACCCTCTTACATGAAGCGAGGACAAAAGTGTAAGTGCGGTGGTAAATGTAAGTGGACTCGCCCATGGGTTGGG[T/C]
TGGCACCTTCTTCCCCGGCACCGGTATCTGCCTCTGCCGTTGATTATTCCTTCTCCAGTGGGCTCCAAGCCGATTCCCTGCACATGTGTCATCCCAAAAA

Reverse complement sequence

TTTTTGGGATGACACATGTGCAGGGAATCGGCTTGGAGCCCACTGGAGAAGGAATAATCAACGGCAGAGGCAGATACCGGTGCCGGGGAAGAAGGTGCCA[A/G]
CCCAACCCATGGGCGAGTCCACTTACATTTACCACCGCACTTACACTTTTGTCCTCGCTTCATGTAAGAGGGTTAACCCATGAGTGACATGGTTGGAGAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.50% 16.40% 0.11% 0.00% NA
All Indica  2759 81.40% 18.40% 0.14% 0.00% NA
All Japonica  1512 98.80% 1.10% 0.07% 0.00% NA
Aus  269 21.60% 78.40% 0.00% 0.00% NA
Indica I  595 91.10% 8.90% 0.00% 0.00% NA
Indica II  465 79.60% 20.40% 0.00% 0.00% NA
Indica III  913 80.40% 19.30% 0.33% 0.00% NA
Indica Intermediate  786 76.50% 23.40% 0.13% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.50% 0.41% 0.00% NA
VI/Aromatic  96 74.00% 26.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 0.00% 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
vg1218883751 T -> C LOC_Os12g31390.1 missense_variant ; p.Val4Ala; MODERATE nonsynonymous_codon ; V4A Average:66.958; most accessible tissue: Zhenshan97 young leaf, score: 80.325 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218883751 NA 5.83E-06 mr1457 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
vg1218883751 3.62E-06 NA mr1458 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
vg1218883751 NA 1.40E-14 mr1458 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
vg1218883751 NA 1.44E-06 mr1686 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
vg1218883751 NA 1.26E-08 mr1457_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
vg1218883751 1.18E-10 NA mr1458_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
vg1218883751 1.06E-08 7.50E-18 mr1458_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
vg1218883751 NA 9.03E-06 mr1882_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