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Detailed information for vg0613448734:

Variant ID: vg0613448734 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13448734
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTCCGCCCCGTTCGGTATCCCGAACTCGGCCGAGATCTACCCCAAGGTCATCTCCGACGAGTCAGTTTCAAACCACTCGGACGAGATCCAATCTACTT[T/C]
AACACCACCAGATCAAGACGATGGGGCCTACCCGCCAATCCTGATGAAACTCCTCGACGATCTGGCTGCCGTCTTTACTACAAGGGCGTCTTCTCCCCGT

Reverse complement sequence

ACGGGGAGAAGACGCCCTTGTAGTAAAGACGGCAGCCAGATCGTCGAGGAGTTTCATCAGGATTGGCGGGTAGGCCCCATCGTCTTGATCTGGTGGTGTT[A/G]
AAGTAGATTGGATCTCGTCCGAGTGGTTTGAAACTGACTCGTCGGAGATGACCTTGGGGTAGATCTCGGCCGAGTTCGGGATACCGAACGGGGCGGAGAT

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 68.20% 30.80% 1.02% 0.00% NA
All Indica  2759 95.90% 2.50% 1.63% 0.00% NA
All Japonica  1512 10.30% 89.60% 0.07% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 93.60% 2.70% 3.70% 0.00% NA
Indica II  465 95.90% 3.20% 0.86% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 93.60% 4.10% 2.29% 0.00% NA
Temperate Japonica  767 3.80% 96.20% 0.00% 0.00% NA
Tropical Japonica  504 21.20% 78.80% 0.00% 0.00% NA
Japonica Intermediate  241 8.30% 91.30% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 65.60% 32.20% 2.22% 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
vg0613448734 T -> C LOC_Os06g23070.1 missense_variant ; p.Leu81Ser; MODERATE nonsynonymous_codon ; L81S Average:63.081; most accessible tissue: Minghui63 flag leaf, score: 80.241 benign 0.095 TOLERATED 0.49

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613448734 NA 1.28E-21 mr1020 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
vg0613448734 9.05E-20 1.83E-88 mr1033 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
vg0613448734 2.42E-11 5.83E-19 mr1033 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
vg0613448734 NA 2.75E-69 mr1132 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
vg0613448734 2.11E-12 3.66E-48 mr1176 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
vg0613448734 6.12E-08 2.76E-12 mr1176 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
vg0613448734 NA 1.35E-54 mr1178 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
vg0613448734 NA 4.18E-21 mr1477 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
vg0613448734 1.51E-11 8.85E-74 mr1536 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
vg0613448734 3.60E-11 3.60E-11 mr1536 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
vg0613448734 NA 3.29E-13 mr1740 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
vg0613448734 NA 3.98E-21 mr1971 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
vg0613448734 9.52E-26 1.91E-122 mr1033_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
vg0613448734 1.69E-11 2.24E-21 mr1033_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
vg0613448734 6.10E-12 NA mr1536_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
vg0613448734 1.11E-09 3.70E-10 mr1536_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
vg0613448734 NA 2.27E-08 mr1660_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
vg0613448734 NA 3.19E-14 mr1950_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