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Detailed information for vg0729442292:

Variant ID: vg0729442292 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 29442292
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAACCCTGAACGGCGGGAATCGCCTCATCGAGTCACCCCTCCACCTCGCGGCACCGGCGATCTCCGCGATCACCTGAATGGCCACCGAGACACACGACG[C/T]
ACACGAGACAACGAGAACCATTCCCGGCGTCATGTCTCTTCACGGCGTCATGATAATGAAGATCGAGGAGGCCGTTCAAGCGAAGACCGAGACCGTGATA

Reverse complement sequence

TATCACGGTCTCGGTCTTCGCTTGAACGGCCTCCTCGATCTTCATTATCATGACGCCGTGAAGAGACATGACGCCGGGAATGGTTCTCGTTGTCTCGTGT[G/A]
CGTCGTGTGTCTCGGTGGCCATTCAGGTGATCGCGGAGATCGCCGGTGCCGCGAGGTGGAGGGGTGACTCGATGAGGCGATTCCCGCCGTTCAGGGTTTT

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 93.50% 6.50% 0.00% 0.00% NA
All Indica  2759 97.70% 2.30% 0.00% 0.00% NA
All Japonica  1512 95.30% 4.70% 0.00% 0.00% NA
Aus  269 68.00% 32.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 95.10% 4.90% 0.00% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 86.90% 13.10% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 15.60% 84.40% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0729442292 C -> T LOC_Os07g49150.1 upstream_gene_variant ; 2160.0bp to feature; MODIFIER silent_mutation Average:40.625; most accessible tissue: Minghui63 root, score: 60.831 N N N N
vg0729442292 C -> T LOC_Os07g49160.1 intron_variant ; MODIFIER silent_mutation Average:40.625; most accessible tissue: Minghui63 root, score: 60.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729442292 NA 3.83E-06 mr1133 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
vg0729442292 NA 8.39E-06 mr1226 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
vg0729442292 NA 7.89E-06 mr1304 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
vg0729442292 7.04E-06 1.16E-08 mr1364 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
vg0729442292 NA 2.16E-08 mr1443 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
vg0729442292 NA 2.64E-07 mr1498_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