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Detailed information for vg1009450104:

Variant ID: vg1009450104 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9450104
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AGCACTTGACCTTACTATAGCAAACTCGGCCAAAGATGAACCCCTGATGGCAGCTGCTTCCTACTTCTGGTCAAACACCATTAATGCCTTTTTGTTCAAT[C/T]
AAGGGCCGATGACCCCAACTCTCATAGATATCAGCATGATCACGGGTCTGGATGTCACCTCATCGGCCAACCCTATGAGCTTGAACACAAAGAACCAATA

Reverse complement sequence

TATTGGTTCTTTGTGTTCAAGCTCATAGGGTTGGCCGATGAGGTGACATCCAGACCCGTGATCATGCTGATATCTATGAGAGTTGGGGTCATCGGCCCTT[G/A]
ATTGAACAAAAAGGCATTAATGGTGTTTGACCAGAAGTAGGAAGCAGCTGCCATCAGGGGTTCATCTTTGGCCGAGTTTGCTATAGTAAGGTCAAGTGCT

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 66.40% 26.20% 0.57% 6.88% NA
All Indica  2759 59.50% 39.60% 0.33% 0.58% NA
All Japonica  1512 74.50% 5.00% 1.06% 19.38% NA
Aus  269 97.40% 2.20% 0.00% 0.37% NA
Indica I  595 73.40% 25.20% 0.50% 0.84% NA
Indica II  465 40.40% 58.50% 0.43% 0.65% NA
Indica III  913 63.10% 36.40% 0.33% 0.22% NA
Indica Intermediate  786 56.10% 43.00% 0.13% 0.76% NA
Temperate Japonica  767 67.80% 0.40% 1.17% 30.64% NA
Tropical Japonica  504 83.10% 13.50% 0.40% 2.98% NA
Japonica Intermediate  241 78.00% 2.10% 2.07% 17.84% NA
VI/Aromatic  96 45.80% 42.70% 1.04% 10.42% NA
Intermediate  90 68.90% 24.40% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009450104 C -> T LOC_Os10g18630.1 stop_gained ; p.Gln142*; HIGH stop_gained Average:42.94; most accessible tissue: Minghui63 young leaf, score: 68.745 N N N N
vg1009450104 C -> DEL LOC_Os10g18630.1 N frameshift_variant Average:42.94; most accessible tissue: Minghui63 young leaf, score: 68.745 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009450104 1.29E-07 1.23E-11 mr1053 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
vg1009450104 8.47E-09 6.48E-09 mr1053 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
vg1009450104 3.86E-06 NA mr1070 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
vg1009450104 2.71E-06 NA mr1070 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
vg1009450104 6.93E-07 NA mr1128 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
vg1009450104 1.45E-07 3.83E-07 mr1128 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
vg1009450104 NA 4.36E-06 mr1139 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
vg1009450104 NA 4.95E-07 mr1145 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
vg1009450104 4.24E-07 4.53E-07 mr1147 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
vg1009450104 NA 3.11E-06 mr1204 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
vg1009450104 NA 4.90E-06 mr1436 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
vg1009450104 NA 5.58E-07 mr1437 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
vg1009450104 NA 2.41E-12 mr1709 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
vg1009450104 NA 4.66E-10 mr1709 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
vg1009450104 NA 7.98E-07 mr1027_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
vg1009450104 3.28E-07 7.43E-10 mr1053_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
vg1009450104 1.17E-07 3.05E-08 mr1053_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
vg1009450104 4.85E-07 4.39E-13 mr1147_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
vg1009450104 9.24E-07 6.48E-07 mr1147_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
vg1009450104 NA 2.76E-06 mr1250_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
vg1009450104 5.30E-06 1.09E-06 mr1264_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
vg1009450104 NA 1.42E-11 mr1709_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
vg1009450104 NA 9.79E-11 mr1709_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