Search for Variation information by Variation ID:

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

Detailed information for vg0919842296:

Variant ID: vg0919842296 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19842296
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.17, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCGGCCATACTCCACCAACCTAATTCCTCTTGGATACGACTAATCATCTGGTGTACTGTCGCCTCCTTTGCTCTAAAGATTCTTGCATTTCGTTCCTT[C/T]
CAGATTTCCCAAGCAATGAGCAAGAAGAGAGTTCTGAGTCCTTTCTGTTTTGTTGCTTCCAGGTCGCTTGTTCCTTGTGTCCACCAATCTAAGAGGTTTC

Reverse complement sequence

GAAACCTCTTAGATTGGTGGACACAAGGAACAAGCGACCTGGAAGCAACAAAACAGAAAGGACTCAGAACTCTCTTCTTGCTCATTGCTTGGGAAATCTG[G/A]
AAGGAACGAAATGCAAGAATCTTTAGAGCAAAGGAGGCGACAGTACACCAGATGATTAGTCGTATCCAAGAGGAATTAGGTTGGTGGAGTATGGCCGGCG

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 52.60% 40.00% 2.50% 4.93% NA
All Indica  2759 86.00% 7.50% 1.12% 5.40% NA
All Japonica  1512 0.30% 99.30% 0.26% 0.07% NA
Aus  269 31.20% 11.50% 28.62% 28.62% NA
Indica I  595 96.30% 2.90% 0.00% 0.84% NA
Indica II  465 86.90% 6.70% 0.43% 6.02% NA
Indica III  913 85.40% 8.20% 0.88% 5.48% NA
Indica Intermediate  786 78.20% 10.70% 2.67% 8.40% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 99.80% 0.00% 0.20% NA
Japonica Intermediate  241 0.80% 97.50% 1.66% 0.00% NA
VI/Aromatic  96 3.10% 91.70% 3.12% 2.08% NA
Intermediate  90 22.20% 70.00% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0919842296 C -> DEL LOC_Os09g33610.1 N frameshift_variant Average:33.018; most accessible tissue: Minghui63 root, score: 50.524 N N N N
vg0919842296 C -> T LOC_Os09g33610.1 stop_gained ; p.Trp1939*; HIGH stop_gained Average:33.018; most accessible tissue: Minghui63 root, score: 50.524 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919842296 NA 9.73E-06 mr1002 Ind_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
vg0919842296 NA 3.08E-07 mr1029 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
vg0919842296 NA 3.02E-07 mr1042 Ind_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
vg0919842296 NA 1.02E-06 mr1043 Ind_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
vg0919842296 NA 1.12E-09 mr1047 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
vg0919842296 NA 4.36E-11 mr1172 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
vg0919842296 NA 3.20E-06 mr1185 Ind_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
vg0919842296 NA 2.06E-07 mr1189 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
vg0919842296 4.25E-11 3.53E-12 mr1216 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
vg0919842296 1.78E-09 5.84E-16 mr1216 Ind_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
vg0919842296 NA 1.27E-10 mr1325 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
vg0919842296 NA 1.25E-12 mr1326 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
vg0919842296 NA 4.10E-06 mr1502 Ind_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
vg0919842296 NA 3.14E-06 mr1532 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
vg0919842296 NA 1.56E-06 mr1625 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
vg0919842296 NA 1.28E-07 mr1726 Ind_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
vg0919842296 NA 1.95E-08 mr1796 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
vg0919842296 NA 1.24E-06 mr1950 Ind_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
vg0919842296 NA 7.15E-09 mr1990 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
vg0919842296 NA 5.35E-06 mr1676_2 Ind_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
vg0919842296 1.90E-06 NA mr1793_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