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Detailed information for vg0411210100:

Variant ID: vg0411210100 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 11210100
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGCCATAACGACTGAGTTGGGGTGTTCCGATCTTCCAGTGCCAAGGTTCGCGCGTAAAGCACTGGGTTCTCCATCTTCAGGATGGTGTCCTTCTGGGAC[C/T]
ATCTCAACTTCAGGTTGAGTTGCCTCTTCTGGGGCTTTCTCAACTTCAGGTTGAGCTTCTTCAACTGATTCTTTGAGTGGAACAAGTGGCTCAGGTCCTT

Reverse complement sequence

AAGGACCTGAGCCACTTGTTCCACTCAAAGAATCAGTTGAAGAAGCTCAACCTGAAGTTGAGAAAGCCCCAGAAGAGGCAACTCAACCTGAAGTTGAGAT[G/A]
GTCCCAGAAGGACACCATCCTGAAGATGGAGAACCCAGTGCTTTACGCGCGAACCTTGGCACTGGAAGATCGGAACACCCCAACTCAGTCGTTATGGCAA

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 84.50% 14.70% 0.38% 0.42% NA
All Indica  2759 98.30% 0.50% 0.47% 0.69% NA
All Japonica  1512 61.80% 37.90% 0.26% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.00% 0.34% 0.17% NA
Indica II  465 94.20% 1.10% 1.51% 3.23% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 0.90% 0.51% 0.38% NA
Temperate Japonica  767 96.30% 3.70% 0.00% 0.00% NA
Tropical Japonica  504 5.40% 94.00% 0.40% 0.20% NA
Japonica Intermediate  241 69.70% 29.50% 0.83% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 72.20% 26.70% 1.11% 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
vg0411210100 C -> DEL LOC_Os04g20120.1 N frameshift_variant Average:11.209; most accessible tissue: Minghui63 panicle, score: 20.733 N N N N
vg0411210100 C -> T LOC_Os04g20120.1 missense_variant ; p.Met692Ile; MODERATE nonsynonymous_codon ; M692I Average:11.209; most accessible tissue: Minghui63 panicle, score: 20.733 unknown unknown TOLERATED 0.55

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0411210100 NA 2.57E-07 mr1194 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
vg0411210100 NA 2.31E-12 mr1330 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
vg0411210100 NA 3.87E-13 mr1454 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
vg0411210100 NA 9.72E-09 mr1715 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
vg0411210100 NA 4.44E-06 mr1844 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
vg0411210100 NA 2.26E-11 mr1864 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
vg0411210100 NA 1.76E-11 mr1097_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
vg0411210100 NA 2.89E-09 mr1398_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
vg0411210100 NA 2.70E-07 mr1668_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
vg0411210100 NA 7.69E-06 mr1668_2 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