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Detailed information for vg0400034660:

Variant ID: vg0400034660 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 34660
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTGCCGCAACCAACAGGGGGCTAACCAAAGGATCCGCTACACCAATCCCTATCCAGGGGGATCCTCCTCGCAGCAGCAGCAACAGCAGCAGCAACCA[T/C]
GCTCCGCGCCCCGACCTCAATTTGTGGTGCGCGTCCCACAGCCGCAGCAACAGCAGAGTCAACAAGGGACTCGTGCGCCCCGTCCTCCTACGCCAGCCGT

Reverse complement sequence

ACGGCTGGCGTAGGAGGACGGGGCGCACGAGTCCCTTGTTGACTCTGCTGTTGCTGCGGCTGTGGGACGCGCACCACAAATTGAGGTCGGGGCGCGGAGC[A/G]
TGGTTGCTGCTGCTGTTGCTGCTGCTGCGAGGAGGATCCCCCTGGATAGGGATTGGTGTAGCGGATCCTTTGGTTAGCCCCCTGTTGGTTGCGGCAATTT

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 19.60% 4.10% 22.96% 53.32% NA
All Indica  2759 5.50% 1.20% 21.38% 71.95% NA
All Japonica  1512 47.80% 9.20% 10.38% 32.61% NA
Aus  269 9.70% 4.80% 85.13% 0.37% NA
Indica I  595 6.70% 0.00% 16.64% 76.64% NA
Indica II  465 6.70% 0.60% 11.40% 81.29% NA
Indica III  913 2.70% 2.80% 28.15% 66.27% NA
Indica Intermediate  786 7.00% 0.50% 23.03% 69.47% NA
Temperate Japonica  767 72.20% 15.60% 1.69% 10.43% NA
Tropical Japonica  504 17.30% 2.40% 24.60% 55.75% NA
Japonica Intermediate  241 34.00% 2.90% 8.30% 54.77% NA
VI/Aromatic  96 3.10% 6.20% 84.38% 6.25% NA
Intermediate  90 25.60% 4.40% 31.11% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0400034660 T -> C LOC_Os04g01040.1 missense_variant ; p.Cys590Arg; MODERATE nonsynonymous_codon ; C590R Average:33.009; most accessible tissue: Minghui63 young leaf, score: 51.901 probably damaging -2.729 TOLERATED 1.00
vg0400034660 T -> DEL LOC_Os04g01040.1 N frameshift_variant Average:33.009; most accessible tissue: Minghui63 young leaf, score: 51.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0400034660 1.97E-06 1.97E-06 mr1166_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
vg0400034660 1.06E-06 NA mr1305_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
vg0400034660 4.65E-08 2.39E-08 mr1305_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
vg0400034660 NA 3.42E-06 mr1409_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
vg0400034660 6.11E-06 3.25E-06 mr1559_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
vg0400034660 3.09E-07 7.53E-07 mr1585_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
vg0400034660 3.53E-06 NA mr1670_2 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
vg0400034660 4.65E-08 4.65E-08 mr1670_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
vg0400034660 6.69E-07 2.13E-07 mr1765_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