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Detailed information for vg1004555361:

Variant ID: vg1004555361 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4555361
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


ACGTCGCCTTGGGGTGTTCCGGTAATCTTTGTGGAAAAGAAAGACAAAACCAAGAGGATGTGTGTTGACTACCGCACGCTCAATGAGGTCACTATTAAGA[A/T]
CAAGTACCCTTTGCCAAGGATTGATGATCTGTTTGATCAGTTGAAAGGAGCTACTATGTTCTCTAAGATAGACCTGCGATCAGGCTATCACCAGTTGAGG

Reverse complement sequence

CCTCAACTGGTGATAGCCTGATCGCAGGTCTATCTTAGAGAACATAGTAGCTCCTTTCAACTGATCAAACAGATCATCAATCCTTGGCAAAGGGTACTTG[T/A]
TCTTAATAGTGACCTCATTGAGCGTGCGGTAGTCAACACACATCCTCTTGGTTTTGTCTTTCTTTTCCACAAAGATTACCGGAACACCCCAAGGCGACGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 31.00% 25.10% 1.99% 41.94% NA
All Indica  2759 13.80% 41.30% 2.32% 42.59% NA
All Japonica  1512 65.40% 1.10% 1.39% 32.14% NA
Aus  269 4.10% 2.60% 1.12% 92.19% NA
Indica I  595 2.70% 40.80% 2.69% 53.78% NA
Indica II  465 16.10% 48.60% 1.94% 33.33% NA
Indica III  913 22.00% 41.30% 1.86% 34.83% NA
Indica Intermediate  786 11.30% 37.30% 2.80% 48.60% NA
Temperate Japonica  767 93.70% 0.90% 0.39% 4.95% NA
Tropical Japonica  504 19.20% 0.60% 2.98% 77.18% NA
Japonica Intermediate  241 71.80% 2.50% 1.24% 24.48% NA
VI/Aromatic  96 53.10% 1.00% 5.21% 40.62% NA
Intermediate  90 34.40% 26.70% 1.11% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004555361 A -> T LOC_Os10g08390.1 missense_variant ; p.Asn421Ile; MODERATE nonsynonymous_codon Average:29.243; most accessible tissue: Minghui63 flag leaf, score: 69.182 benign 0.858 DELETERIOUS 0.00
vg1004555361 A -> DEL LOC_Os10g08390.1 N frameshift_variant Average:29.243; most accessible tissue: Minghui63 flag leaf, score: 69.182 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004555361 NA 4.02E-07 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
vg1004555361 NA 1.21E-08 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
vg1004555361 NA 1.70E-06 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
vg1004555361 8.15E-06 8.15E-06 mr1151_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
vg1004555361 NA 5.79E-06 mr1220_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
vg1004555361 NA 3.01E-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
vg1004555361 NA 5.33E-06 mr1308_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
vg1004555361 1.18E-06 1.18E-06 mr1433_2 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
vg1004555361 NA 4.50E-06 mr1691_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
vg1004555361 NA 3.70E-06 mr1729_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
vg1004555361 NA 1.09E-06 mr1852_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
vg1004555361 NA 7.78E-06 mr1887_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