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Detailed information for vg0527589502:

Variant ID: vg0527589502 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27589502
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCGTCTCGGTCTGCCTCATCCTCAACCTCCCTACTCCGGTGTGCAGGCGACAAAGTCCATGGAGGGACATGCTCCATGGGAGACACTGAATCCCCTCT[T/C]
ACACGAAGCTCCTGGCGTCGATTTCTCCATAGCTTATTCTGTGAGTGATGAAGAATTCCTCCATAGGAGCAATTTCGGTAAAGCTATCCCTGATTCGTTC

Reverse complement sequence

GAACGAATCAGGGATAGCTTTACCGAAATTGCTCCTATGGAGGAATTCTTCATCACTCACAGAATAAGCTATGGAGAAATCGACGCCAGGAGCTTCGTGT[A/G]
AGAGGGGATTCAGTGTCTCCCATGGAGCATGTCCCTCCATGGACTTTGTCGCCTGCACACCGGAGTAGGGAGGTTGAGGATGAGGCAGACCGAGACGACG

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 20.30% 0.80% 9.31% 69.61% NA
All Indica  2759 1.10% 1.00% 14.79% 83.11% NA
All Japonica  1512 58.90% 0.30% 0.79% 39.95% NA
Aus  269 0.40% 0.40% 3.35% 95.91% NA
Indica I  595 0.30% 1.30% 8.07% 90.25% NA
Indica II  465 2.60% 0.60% 19.78% 76.99% NA
Indica III  913 0.70% 1.00% 13.80% 84.56% NA
Indica Intermediate  786 1.40% 0.90% 18.07% 79.64% NA
Temperate Japonica  767 96.70% 0.10% 0.00% 3.13% NA
Tropical Japonica  504 2.00% 0.60% 1.98% 95.44% NA
Japonica Intermediate  241 57.70% 0.40% 0.83% 41.08% NA
VI/Aromatic  96 21.90% 3.10% 5.21% 69.79% NA
Intermediate  90 16.70% 1.10% 6.67% 75.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0527589502 T -> DEL LOC_Os05g48130.1 N frameshift_variant Average:24.525; most accessible tissue: Minghui63 panicle, score: 38.588 N N N N
vg0527589502 T -> C LOC_Os05g48130.1 missense_variant ; p.Leu116Ser; MODERATE nonsynonymous_codon ; L116S Average:24.525; most accessible tissue: Minghui63 panicle, score: 38.588 benign -1.097 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527589502 NA 5.60E-22 mr1115 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
vg0527589502 NA 6.97E-17 mr1115 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
vg0527589502 NA 2.89E-52 mr1241 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
vg0527589502 NA 2.74E-11 mr1241 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
vg0527589502 NA 5.29E-06 mr1448 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
vg0527589502 NA 1.28E-22 mr1611 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
vg0527589502 NA 9.62E-14 mr1611 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
vg0527589502 NA 2.81E-07 mr1742 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
vg0527589502 NA 4.36E-12 mr1879 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
vg0527589502 NA 1.83E-22 mr1920 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
vg0527589502 NA 4.15E-12 mr1920 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
vg0527589502 NA 2.21E-07 mr1047_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
vg0527589502 NA 6.10E-09 mr1189_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
vg0527589502 NA 9.35E-62 mr1241_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
vg0527589502 NA 9.10E-13 mr1241_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
vg0527589502 NA 1.90E-06 mr1268_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
vg0527589502 NA 2.74E-07 mr1446_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
vg0527589502 NA 1.15E-08 mr1454_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
vg0527589502 NA 3.34E-09 mr1471_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
vg0527589502 NA 6.50E-12 mr1471_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
vg0527589502 NA 4.88E-10 mr1530_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
vg0527589502 NA 2.83E-09 mr1543_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
vg0527589502 NA 1.75E-22 mr1611_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
vg0527589502 NA 2.56E-10 mr1642_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
vg0527589502 NA 3.04E-11 mr1789_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
vg0527589502 NA 5.34E-08 mr1808_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
vg0527589502 NA 3.43E-08 mr1879_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
vg0527589502 NA 1.75E-14 mr1902_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