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Detailed information for vg0509836819:

Variant ID: vg0509836819 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 9836819
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TATTCTAACACATTTATGCATTGCAAACATCACTAGTTCTCCTCTATTTTGGTAATATTGACGGTCGAAACTGATCGATAATGACCGTCAACAAAGACAT[T/A]
CCTCGTTTTGGCATCTTCCTCTTGCATCAAAACGGCACCAATGACTTCGTCTTCGGAGGCAATATATAACCGAAATGGCTTTCCAGCATTAGGCGCTCGT

Reverse complement sequence

ACGAGCGCCTAATGCTGGAAAGCCATTTCGGTTATATATTGCCTCCGAAGACGAAGTCATTGGTGCCGTTTTGATGCAAGAGGAAGATGCCAAAACGAGG[A/T]
ATGTCTTTGTTGACGGTCATTATCGATCAGTTTCGACCGTCAATATTACCAAAATAGAGGAGAACTAGTGATGTTTGCAATGCATAAATGTGTTAGAATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.80% 13.50% 12.65% 0.00% NA
All Indica  2759 83.00% 3.60% 13.37% 0.00% NA
All Japonica  1512 50.90% 35.10% 14.02% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 58.30% 10.30% 31.43% 0.00% NA
Indica II  465 81.50% 2.80% 15.70% 0.00% NA
Indica III  913 99.30% 0.10% 0.55% 0.00% NA
Indica Intermediate  786 83.70% 3.10% 13.23% 0.00% NA
Temperate Japonica  767 22.30% 60.00% 17.73% 0.00% NA
Tropical Japonica  504 86.30% 6.20% 7.54% 0.00% NA
Japonica Intermediate  241 68.00% 16.20% 15.77% 0.00% NA
VI/Aromatic  96 97.90% 0.00% 2.08% 0.00% NA
Intermediate  90 76.70% 8.90% 14.44% 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
vg0509836819 T -> A LOC_Os05g17170.1 missense_variant ; p.Asn514Tyr; MODERATE nonsynonymous_codon Average:31.411; most accessible tissue: Zhenshan97 young leaf, score: 50.669 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0509836819 NA 4.90E-09 mr1137 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
vg0509836819 NA 4.16E-06 mr1164 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
vg0509836819 NA 2.37E-06 mr1330 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
vg0509836819 NA 4.40E-09 mr1486 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
vg0509836819 NA 5.08E-06 mr1521 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
vg0509836819 NA 4.44E-06 mr1530 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
vg0509836819 NA 8.88E-08 mr1548 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
vg0509836819 NA 2.92E-06 mr1576 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
vg0509836819 NA 1.16E-06 mr1596 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
vg0509836819 NA 2.15E-07 mr1617 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
vg0509836819 NA 2.38E-11 mr1627 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
vg0509836819 NA 2.07E-06 mr1748 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
vg0509836819 NA 2.03E-06 mr1977 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
vg0509836819 NA 3.69E-08 mr1137_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
vg0509836819 NA 1.38E-13 mr1182_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
vg0509836819 NA 1.20E-06 mr1182_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
vg0509836819 NA 4.65E-10 mr1282_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
vg0509836819 NA 7.86E-06 mr1617_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