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Detailed information for vg0321577849:

Variant ID: vg0321577849 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21577849
Reference Allele: CAlternative Allele: T,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGCATCGTAGACTTGGACATGTTGGTTTTGATCATCTCACTAGGTTAAGTGGTTTGGATCTTGCTCGTGGTTTGCCTAAACTTAAGAAAGATTTTGATT[C/T,A]
GGTTTGTTCACTGTGTCGTCATGCTAAGATGGTTGCTTCTTCACATGCTCCTATTGTTTTTTGTGATGACGGATGCACCGGGACAGCTATTACACATAGA

Reverse complement sequence

TCTATGTGTAATAGCTGTCCCGGTGCATCCGTCATCACAAAAAACAATAGGAGCATGTGAAGAAGCAACCATCTTAGCATGACGACACAGTGAACAAACC[G/A,T]
AATCAAAATCTTTCTTAAGTTTAGGCAAACCACGAGCAAGATCCAAACCACTTAACCTAGTGAGATGATCAAAACCAACATGTCCAAGTCTACGATGCCA

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 66.20% 33.70% 0.04% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 9.40% 90.60% 0.00% 0.00% NA
Aus  269 58.70% 41.30% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 95.90% 4.10% 0.00% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 10.10% 89.90% 0.00% 0.00% NA
Japonica Intermediate  241 35.30% 64.70% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 55.60% 42.20% 2.22% 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
vg0321577849 C -> T LOC_Os03g38850.1 N nonsynonymous_codon ; S839L Average:17.186; most accessible tissue: Callus, score: 28.887 unknown unknown TOLERATED 0.13
vg0321577849 C -> A LOC_Os03g38850.1 stop_gained&splice_region_variant ; p.Ser839*; HIGH N Average:17.186; most accessible tissue: Callus, score: 28.887 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321577849 NA 2.41E-21 mr1627 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
vg0321577849 1.92E-06 NA mr1750 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
vg0321577849 NA 7.53E-21 mr1253_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
vg0321577849 NA 6.84E-20 mr1255_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
vg0321577849 7.87E-06 7.87E-06 mr1312_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
vg0321577849 NA 1.50E-25 mr1350_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
vg0321577849 5.90E-06 5.90E-06 mr1645_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
vg0321577849 4.02E-06 4.02E-06 mr1647_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
vg0321577849 2.78E-06 2.78E-06 mr1657_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
vg0321577849 NA 6.57E-11 mr1761_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