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Detailed information for vg1124715978:

Variant ID: vg1124715978 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24715978
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTGTAATGTTAGATCAGTGAGCATATTTGGATACAGGGAACAGATGCTTCCTATTTCTGACTTGAATGTTTTCAGAGTGCTTCATATAGAGAGTGGTA[A/C]
TAAGATGATGGAGATTTGTGGAATTGGGAAGCTACTTCAGTTGCGGTACTTACGGATTGATCTAGTTACACATCTTACTGAAGAAATAGGAGAACTGCTG

Reverse complement sequence

CAGCAGTTCTCCTATTTCTTCAGTAAGATGTGTAACTAGATCAATCCGTAAGTACCGCAACTGAAGTAGCTTCCCAATTCCACAAATCTCCATCATCTTA[T/G]
TACCACTCTCTATATGAAGCACTCTGAAAACATTCAAGTCAGAAATAGGAAGCATCTGTTCCCTGTATCCAAATATGCTCACTGATCTAACATTACAAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 8.00% 0.34% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 80.10% 18.80% 1.06% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 88.90% 10.80% 0.26% 0.00% NA
Tropical Japonica  504 65.70% 31.70% 2.58% 0.00% NA
Japonica Intermediate  241 82.20% 17.40% 0.41% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 0.00% 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
vg1124715978 A -> C LOC_Os11g41210.1 missense_variant ; p.Asn119Thr; MODERATE nonsynonymous_codon Average:52.676; most accessible tissue: Callus, score: 78.004 unknown unknown TOLERATED 0.26

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124715978 NA 5.05E-06 mr1169_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
vg1124715978 NA 2.39E-08 mr1195_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
vg1124715978 1.27E-06 NA mr1579_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
vg1124715978 2.40E-07 NA 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
vg1124715978 6.07E-07 NA mr1841_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
vg1124715978 7.37E-07 NA mr1900_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