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Detailed information for vg0319141942:

Variant ID: vg0319141942 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19141942
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTTCCGGTTGAAGAGCACAGAGAAATCACGTGAAATATCAAAAATGCCCTTGGGCCCACATGTCGGCACAGTGGAGAGATTTGTGGCGTGGTTGTGCGC[T/C]
GAGATGGAGGTGCTCGGCGTGCTTTGTGTGGCGGCGGACCGGCACCGGTGCCGCGAAGCGCTGTCGCACGCGGCGGTGCGTGCTGCGATGGACGTCGTGG

Reverse complement sequence

CCACGACGTCCATCGCAGCACGCACCGCCGCGTGCGACAGCGCTTCGCGGCACCGGTGCCGGTCCGCCGCCACACAAAGCACGCCGAGCACCTCCATCTC[A/G]
GCGCACAACCACGCCACAAATCTCTCCACTGTGCCGACATGTGGGCCCAAGGGCATTTTTGATATTTCACGTGATTTCTCTGTGCTCTTCAACCGGAAAT

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 85.70% 11.30% 2.92% 0.00% NA
All Indica  2759 99.50% 0.40% 0.14% 0.00% NA
All Japonica  1512 57.90% 33.70% 8.40% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.30% 0.38% 0.00% NA
Temperate Japonica  767 30.10% 56.50% 13.43% 0.00% NA
Tropical Japonica  504 90.70% 6.90% 2.38% 0.00% NA
Japonica Intermediate  241 77.60% 17.40% 4.98% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 81.10% 12.20% 6.67% 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
vg0319141942 T -> C LOC_Os03g33509.1 upstream_gene_variant ; 3218.0bp to feature; MODIFIER silent_mutation Average:67.327; most accessible tissue: Zhenshan97 young leaf, score: 84.235 N N N N
vg0319141942 T -> C LOC_Os03g33500.1 intron_variant ; MODIFIER silent_mutation Average:67.327; most accessible tissue: Zhenshan97 young leaf, score: 84.235 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319141942 NA 1.72E-11 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0319141942 5.09E-07 NA mr1354 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
vg0319141942 NA 5.69E-06 mr1354 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
vg0319141942 NA 1.52E-07 mr1829 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
vg0319141942 NA 6.27E-09 mr1002_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
vg0319141942 NA 6.37E-06 mr1332_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
vg0319141942 6.88E-09 NA mr1354_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
vg0319141942 3.39E-06 3.18E-06 mr1354_2 Jap_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
vg0319141942 NA 2.93E-08 mr1576_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
vg0319141942 NA 5.92E-07 mr1648_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