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Detailed information for vg0722707172:

Variant ID: vg0722707172 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22707172
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCACTCGCGAAGTTAATGGCCGCATCTCACTACGCGTATCAAGTGCTCAAGATGCTGGGACCGAAGGGAACAATCACTATTCAAGGGAATGCTAAGCTGG[T/C]
AGTGCAATGCGACAAGCGGAGCGTCGACATGGTCGAGCACACGCCCAGCCCACCCGACACAGCCGAGCCACCCAAGAAACTGAGCAAAACAAACAAGACG

Reverse complement sequence

CGTCTTGTTTGTTTTGCTCAGTTTCTTGGGTGGCTCGGCTGTGTCGGGTGGGCTGGGCGTGTGCTCGACCATGTCGACGCTCCGCTTGTCGCATTGCACT[A/G]
CCAGCTTAGCATTCCCTTGAATAGTGATTGTTCCCTTCGGTCCCAGCATCTTGAGCACTTGATACGCGTAGTGAGATGCGGCCATTAACTTCGCGAGTGC

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 89.50% 8.40% 2.09% 0.00% NA
All Indica  2759 89.50% 9.70% 0.80% 0.00% NA
All Japonica  1512 93.30% 1.80% 4.96% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 83.90% 14.00% 2.15% 0.00% NA
Indica III  913 83.40% 16.10% 0.55% 0.00% NA
Indica Intermediate  786 92.20% 6.90% 0.89% 0.00% NA
Temperate Japonica  767 88.40% 2.20% 9.39% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 3.70% 1.24% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 83.30% 14.40% 2.22% 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
vg0722707172 T -> C LOC_Os07g37860.1 missense_variant ; p.Val963Ala; MODERATE nonsynonymous_codon ; V963A Average:43.893; most accessible tissue: Minghui63 young leaf, score: 59.171 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722707172 NA 3.81E-10 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0722707172 NA 1.26E-06 mr1071 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
vg0722707172 NA 9.20E-06 mr1080 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
vg0722707172 NA 7.36E-06 mr1203 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
vg0722707172 NA 7.53E-06 mr1382 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
vg0722707172 NA 1.77E-07 mr1829 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
vg0722707172 1.27E-08 7.47E-14 mr1829_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
vg0722707172 NA 2.93E-06 mr1829_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
vg0722707172 7.04E-08 NA mr1842_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