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Detailed information for vg1002726149:

Variant ID: vg1002726149 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2726149
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGCGCATAAAATTAACTAAAAGGTTCAACAACAAAGCAAGATTTCACATGTGCTACTGATTCATACAAAAATATTGTCTTTTATATTATCACTATTTAT[T/A]
TATGTTCCTAATTGATTTCTGATAAATCCTGTACATTTTTATATGTTAATTTGACAACCTATAACATATATATTACCAGTTAATTTAAGTATTTCCACTA

Reverse complement sequence

TAGTGGAAATACTTAAATTAACTGGTAATATATATGTTATAGGTTGTCAAATTAACATATAAAAATGTACAGGATTTATCAGAAATCAATTAGGAACATA[A/T]
ATAAATAGTGATAATATAAAAGACAATATTTTTGTATGAATCAGTAGCACATGTGAAATCTTGCTTTGTTGTTGAACCTTTTAGTTAATTTTATGCGCTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.30% 0.04% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 81.20% 18.70% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 69.90% 29.90% 0.26% 0.00% NA
Tropical Japonica  504 95.40% 4.60% 0.00% 0.00% NA
Japonica Intermediate  241 87.10% 12.90% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1002726149 T -> A LOC_Os10g05510-LOC_Os10g05520 intergenic_region ; MODIFIER silent_mutation Average:21.201; most accessible tissue: Zhenshan97 young leaf, score: 47.986 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002726149 5.47E-07 9.20E-06 mr1040 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
vg1002726149 NA 2.42E-06 mr1210 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
vg1002726149 NA 6.78E-06 mr1305 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
vg1002726149 NA 1.35E-06 mr1585 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
vg1002726149 NA 2.65E-06 mr1586 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
vg1002726149 NA 8.69E-06 mr1736 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
vg1002726149 NA 2.30E-07 mr1585_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