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Detailed information for vg0721447322:

Variant ID: vg0721447322 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 21447322
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCCAGATAAGTAAGGACAAGTAGAGTTCTATATGAAAACTATATGGACTACTCAAATTGTATCCATATTGGTATTTGTAGTTATGTTTGGACAATGGGA[C/T]
ATCTATGGGTATAAATACAAGACCCCCTAAAGAAGGGGGAGGAGACCAACACAAGCCAAGACAAAGCCAGATATCGACATCAGAGATTAGCCTAGACAGA

Reverse complement sequence

TCTGTCTAGGCTAATCTCTGATGTCGATATCTGGCTTTGTCTTGGCTTGTGTTGGTCTCCTCCCCCTTCTTTAGGGGGTCTTGTATTTATACCCATAGAT[G/A]
TCCCATTGTCCAAACATAACTACAAATACCAATATGGATACAATTTGAGTAGTCCATATAGTTTTCATATAGAACTCTACTTGTCCTTACTTATCTGGAA

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 82.70% 15.90% 1.40% 0.00% NA
All Indica  2759 97.60% 2.30% 0.11% 0.00% NA
All Japonica  1512 53.80% 42.10% 4.03% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 96.40% 3.40% 0.22% 0.00% NA
Indica Intermediate  786 97.50% 2.40% 0.13% 0.00% NA
Temperate Japonica  767 70.90% 21.30% 7.82% 0.00% NA
Tropical Japonica  504 28.60% 71.40% 0.00% 0.00% NA
Japonica Intermediate  241 52.30% 47.30% 0.41% 0.00% NA
VI/Aromatic  96 63.50% 34.40% 2.08% 0.00% NA
Intermediate  90 80.00% 20.00% 0.00% 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
vg0721447322 C -> T LOC_Os07g35810.1 upstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:53.28; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0721447322 C -> T LOC_Os07g35820.1 downstream_gene_variant ; 765.0bp to feature; MODIFIER silent_mutation Average:53.28; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N
vg0721447322 C -> T LOC_Os07g35810-LOC_Os07g35820 intergenic_region ; MODIFIER silent_mutation Average:53.28; most accessible tissue: Zhenshan97 young leaf, score: 75.039 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0721447322 NA 2.97E-06 mr1248 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
vg0721447322 8.69E-07 8.70E-07 mr1572 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
vg0721447322 NA 1.47E-07 mr1779 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
vg0721447322 5.63E-06 5.71E-06 mr1899 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
vg0721447322 1.44E-06 1.44E-06 mr1899 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
vg0721447322 NA 1.24E-06 mr1369_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
vg0721447322 NA 8.71E-06 mr1420_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
vg0721447322 NA 3.92E-07 mr1453_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
vg0721447322 NA 5.20E-07 mr1510_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
vg0721447322 NA 2.56E-06 mr1524_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
vg0721447322 NA 7.16E-11 mr1851_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
vg0721447322 NA 1.07E-13 mr1864_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