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Detailed information for vg0611943788:

Variant ID: vg0611943788 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11943788
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACATACTGATATTTGGGACAAACCTTGGGGTGATAAATGAGGTTAAATCATTTTTGTCTCAAAATTTTGATATGAAGGATTTGGGAGTAGCTGATGTTA[C/T]
CTTAAACATTAAGCTAATTAGAGGTGAGAATGGGATTACACTCTTGCAATCCCATTATGTCGAGAAGATCTTGAATCGCTTTGGCTACATTGATAGTAAG

Reverse complement sequence

CTTACTATCAATGTAGCCAAAGCGATTCAAGATCTTCTCGACATAATGGGATTGCAAGAGTGTAATCCCATTCTCACCTCTAATTAGCTTAATGTTTAAG[G/A]
TAACATCAGCTACTCCCAAATCCTTCATATCAAAATTTTGAGACAAAAATGATTTAACCTCATTTATCACCCCAAGGTTTGTCCCAAATATCAGTATGTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.80% 31.20% 0.06% 2.86% NA
All Indica  2759 96.10% 1.90% 0.04% 1.99% NA
All Japonica  1512 11.10% 88.60% 0.00% 0.33% NA
Aus  269 86.60% 8.20% 0.00% 5.20% NA
Indica I  595 94.10% 1.70% 0.17% 4.03% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 98.50% 0.40% 0.00% 1.10% NA
Indica Intermediate  786 93.90% 3.40% 0.00% 2.67% NA
Temperate Japonica  767 3.40% 96.60% 0.00% 0.00% NA
Tropical Japonica  504 24.00% 76.00% 0.00% 0.00% NA
Japonica Intermediate  241 8.70% 89.20% 0.00% 2.07% NA
VI/Aromatic  96 13.50% 29.20% 2.08% 55.21% NA
Intermediate  90 52.20% 38.90% 0.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0611943788 C -> T LOC_Os06g20730.1 missense_variant ; p.Thr320Ile; MODERATE nonsynonymous_codon ; T320I Average:32.102; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 possibly damaging -1.796 TOLERATED 1.00
vg0611943788 C -> DEL LOC_Os06g20730.1 N frameshift_variant Average:32.102; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611943788 NA 4.19E-22 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
vg0611943788 NA 9.58E-74 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
vg0611943788 NA 7.44E-11 mr1138 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
vg0611943788 NA 6.03E-40 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
vg0611943788 NA 1.14E-20 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
vg0611943788 NA 1.29E-19 mr1541 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
vg0611943788 NA 4.37E-25 mr1631 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
vg0611943788 NA 1.32E-08 mr1637 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
vg0611943788 NA 3.97E-13 mr1035_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
vg0611943788 NA 1.77E-69 mr1087_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
vg0611943788 NA 2.97E-07 mr1212_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
vg0611943788 NA 7.38E-12 mr1216_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
vg0611943788 NA 2.12E-19 mr1276_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
vg0611943788 NA 1.93E-14 mr1333_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
vg0611943788 NA 1.58E-07 mr1783_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
vg0611943788 NA 1.11E-07 mr1837_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