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Detailed information for vg1202557972:

Variant ID: vg1202557972 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2557972
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAAATTGTTGAGACTTGCAAAGTTTCTTTTGATGAGGCTAGTCCAGGTACTAGACCCGATATTGCAGGTACACTGTCACAGGTTCAGGGGGAGGATGAT[T/C]
GTATTTTTGAAGACGAGAGCAACGACAACGACAACGACAAGGTCGGCTCGGCCGGTTAGACCGGGCGCCAGGCCGGTCAGACCGCCGGCACACCTCCGGT

Reverse complement sequence

ACCGGAGGTGTGCCGGCGGTCTGACCGGCCTGGCGCCCGGTCTAACCGGCCGAGCCGACCTTGTCGTTGTCGTTGTCGTTGCTCTCGTCTTCAAAAATAC[A/G]
ATCATCCTCCCCCTGAACCTGTGACAGTGTACCTGCAATATCGGGTCTAGTACCTGGACTAGCCTCATCAAAAGAAACTTTGCAAGTCTCAACAATTTTG

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 56.90% 37.40% 4.13% 1.57% NA
All Indica  2759 92.90% 2.80% 2.86% 1.52% NA
All Japonica  1512 2.20% 97.70% 0.07% 0.07% NA
Aus  269 24.20% 24.20% 42.01% 9.67% NA
Indica I  595 99.30% 0.30% 0.34% 0.00% NA
Indica II  465 83.40% 4.90% 5.38% 6.24% NA
Indica III  913 94.70% 1.50% 3.29% 0.44% NA
Indica Intermediate  786 91.30% 4.70% 2.80% 1.15% NA
Temperate Japonica  767 3.40% 96.60% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.60% 0.00% 0.20% NA
Japonica Intermediate  241 0.40% 99.20% 0.41% 0.00% NA
VI/Aromatic  96 1.00% 95.80% 2.08% 1.04% NA
Intermediate  90 33.30% 62.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1202557972 T -> C LOC_Os12g05570.1 missense_variant ; p.Cys435Arg; MODERATE nonsynonymous_codon ; C435R Average:39.455; most accessible tissue: Minghui63 root, score: 51.763 unknown unknown TOLERATED 0.46
vg1202557972 T -> DEL LOC_Os12g05570.1 N frameshift_variant Average:39.455; most accessible tissue: Minghui63 root, score: 51.763 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202557972 NA 5.37E-25 mr1571 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
vg1202557972 NA 5.88E-11 mr1609 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
vg1202557972 NA 3.59E-44 mr1070_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
vg1202557972 NA 2.83E-74 mr1088_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
vg1202557972 NA 1.59E-34 mr1181_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
vg1202557972 NA 2.97E-37 mr1224_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
vg1202557972 NA 2.14E-38 mr1264_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
vg1202557972 NA 7.09E-22 mr1609_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
vg1202557972 2.85E-07 NA mr1865_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