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

Detailed information for vg0401802995:

Variant ID: vg0401802995 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1802995
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


TTCACAGTTAAGTCTTGCTGAGAAGGAAACAAGGTCGTCAAAGACAGCCACTCGGGAGACTTACATTTACAATGCGGGTAGCTTCTCCGAGTGCTTTCTT[T/C]
AGCTGGCGCACCTCTTCGTCTTCCTTTTGTCGGTTTATGACGATGCCCGCAGGTTGCAAGTTGTTGTCCCACCATTTGATTAAGATGGGGGGACGAGAAT

Reverse complement sequence

ATTCTCGTCCCCCCATCTTAATCAAATGGTGGGACAACAACTTGCAACCTGCGGGCATCGTCATAAACCGACAAAAGGAAGACGAAGAGGTGCGCCAGCT[A/G]
AAGAAAGCACTCGGAGAAGCTACCCGCATTGTAAATGTAAGTCTCCCGAGTGGCTGTCTTTGACGACCTTGTTTCCTTCTCAGCAAGACTTAACTGTGAA

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 49.60% 15.20% 5.76% 29.45% NA
All Indica  2759 45.10% 2.40% 6.34% 46.14% NA
All Japonica  1512 55.40% 41.90% 0.20% 2.58% NA
Aus  269 43.10% 1.90% 34.20% 20.82% NA
Indica I  595 32.10% 2.90% 10.25% 54.79% NA
Indica II  465 50.10% 2.80% 3.87% 43.23% NA
Indica III  913 52.40% 0.20% 4.05% 43.37% NA
Indica Intermediate  786 43.60% 4.30% 7.51% 44.53% NA
Temperate Japonica  767 26.20% 72.00% 0.26% 1.56% NA
Tropical Japonica  504 90.90% 4.20% 0.20% 4.76% NA
Japonica Intermediate  241 73.90% 24.90% 0.00% 1.24% NA
VI/Aromatic  96 96.90% 0.00% 0.00% 3.12% NA
Intermediate  90 58.90% 15.60% 2.22% 23.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401802995 T -> C LOC_Os04g03950.1 synonymous_variant ; p.Leu531Leu; LOW synonymous_codon Average:28.393; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N
vg0401802995 T -> DEL LOC_Os04g03950.1 N frameshift_variant Average:28.393; most accessible tissue: Minghui63 young leaf, score: 49.581 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401802995 2.72E-06 1.80E-14 mr1182 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
vg0401802995 NA 3.01E-07 mr1182 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
vg0401802995 8.90E-06 1.30E-12 mr1282 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
vg0401802995 NA 3.26E-06 mr1282 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
vg0401802995 4.73E-07 2.49E-15 mr1650 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
vg0401802995 NA 6.22E-07 mr1650 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
vg0401802995 NA 2.69E-11 mr1658 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
vg0401802995 NA 1.14E-11 mr1667 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
vg0401802995 NA 1.14E-06 mr1881 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
vg0401802995 3.17E-06 NA mr1060_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
vg0401802995 NA 1.61E-06 mr1693_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