Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0324374395:

Variant ID: vg0324374395 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24374395
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCCTCAACGGAGTATTCCTGTCTCTTGTGTTTGAGTGCAGTACCGAAACTTCTCCATGATGGAGGTAGTTTCGCAATAATGCACCCGGCCACAAATTTGT[T/C]
GAGTAAGACACACTTAAGGAGTTCGAGTTCCTTAGCCATGGTTTGTATCTCATGAGCCTGTTTGACTACAGAACGGTTGTCAGCCATCTTGTAGTCATGA

Reverse complement sequence

TCATGACTACAAGATGGCTGACAACCGTTCTGTAGTCAAACAGGCTCATGAGATACAAACCATGGCTAAGGAACTCGAACTCCTTAAGTGTGTCTTACTC[A/G]
ACAAATTTGTGGCCGGGTGCATTATTGCGAAACTACCTCCATCATGGAGAAGTTTCGGTACTGCACTCAAACACAAGAGACAGGAATACTCCGTTGAGGG

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 64.00% 35.80% 0.17% 0.00% NA
All Indica  2759 97.70% 2.10% 0.18% 0.00% NA
All Japonica  1512 1.90% 98.10% 0.00% 0.00% NA
Aus  269 93.70% 5.20% 1.12% 0.00% NA
Indica I  595 98.20% 1.50% 0.34% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 4.60% 0.38% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 4.80% 95.20% 0.00% 0.00% NA
Japonica Intermediate  241 0.80% 99.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 45.60% 54.40% 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
vg0324374395 T -> C LOC_Os03g43610.1 missense_variant ; p.Asn170Asp; MODERATE nonsynonymous_codon Average:26.844; most accessible tissue: Zhenshan97 flower, score: 36.732 possibly damaging -1.641 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324374395 NA 1.05E-10 mr1281 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
vg0324374395 NA 6.25E-77 mr1718 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
vg0324374395 NA 6.54E-114 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
vg0324374395 9.14E-07 NA mr1866 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
vg0324374395 NA 5.98E-10 mr1905 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
vg0324374395 NA 6.14E-07 mr1915 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