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Detailed information for vg0404570369:

Variant ID: vg0404570369 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4570369
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACTCGTACGAGACGGTGCGAAGTTCTATTGATAGAGCAGGAAAAAATTACAAGATTACAACCCTGGCGGATCGTAACCAGGAAAAATGAAAAAATATAG[C/T]
ACCACCCGCACACCGACAGCGCCAACACACAACCCGGGAGAAGGCTAGCACCGAACCGACTGCCGCTAGACCAACAAAGGAACACAGACAACATTGCCCC

Reverse complement sequence

GGGGCAATGTTGTCTGTGTTCCTTTGTTGGTCTAGCGGCAGTCGGTTCGGTGCTAGCCTTCTCCCGGGTTGTGTGTTGGCGCTGTCGGTGTGCGGGTGGT[G/A]
CTATATTTTTTCATTTTTCCTGGTTACGATCCGCCAGGGTTGTAATCTTGTAATTTTTTCCTGCTCTATCAATAGAACTTCGCACCGTCTCGTACGAGTC

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 93.90% 6.10% 0.00% 0.00% NA
All Indica  2759 92.90% 7.10% 0.00% 0.00% NA
All Japonica  1512 94.60% 5.40% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 85.10% 14.90% 0.00% 0.00% NA
Indica Intermediate  786 92.90% 7.10% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 78.40% 21.60% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0404570369 C -> T LOC_Os04g08480.1 downstream_gene_variant ; 4113.0bp to feature; MODIFIER silent_mutation Average:54.128; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N
vg0404570369 C -> T LOC_Os04g08470.1 intron_variant ; MODIFIER silent_mutation Average:54.128; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404570369 NA 5.66E-06 mr1057 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
vg0404570369 NA 2.73E-06 mr1123 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
vg0404570369 NA 1.86E-06 mr1118_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
vg0404570369 NA 9.06E-06 mr1119_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
vg0404570369 NA 3.28E-06 mr1120_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
vg0404570369 NA 3.91E-07 mr1123_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
vg0404570369 NA 1.25E-07 mr1240_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
vg0404570369 NA 5.68E-06 mr1242_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
vg0404570369 NA 4.67E-06 mr1247_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
vg0404570369 NA 5.60E-06 mr1496_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