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Detailed information for vg0722812632:

Variant ID: vg0722812632 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 22812632
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGACCCACATGTCAGTTTCACACACAAATTAATAAAAAATGACGGGGCCCACGTGGGCCCCACATGTCATTTCACCCCTCTTCTTCCTCCTCTCTCTC[C/T]
CCATCTCCCATCTCTTCATCTCTCTCCCCTTTCCTCTCTCGCTTCGGTGCTCGCCCCGCTCTCCTCGTCCCCAGGCCTCTCCGACCGCCTCCTCGCCGCC

Reverse complement sequence

GGCGGCGAGGAGGCGGTCGGAGAGGCCTGGGGACGAGGAGAGCGGGGCGAGCACCGAAGCGAGAGAGGAAAGGGGAGAGAGATGAAGAGATGGGAGATGG[G/A]
GAGAGAGAGGAGGAAGAAGAGGGGTGAAATGACATGTGGGGCCCACGTGGGCCCCGTCATTTTTTATTAATTTGTGTGTGAAACTGACATGTGGGTCCCA

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 98.10% 1.90% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 94.00% 6.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 88.80% 11.20% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0722812632 C -> T LOC_Os07g38050.1 upstream_gene_variant ; 2762.0bp to feature; MODIFIER silent_mutation Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0722812632 C -> T LOC_Os07g38030.1 downstream_gene_variant ; 3248.0bp to feature; MODIFIER silent_mutation Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0722812632 C -> T LOC_Os07g38040.1 downstream_gene_variant ; 651.0bp to feature; MODIFIER silent_mutation Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0722812632 C -> T LOC_Os07g38060.1 downstream_gene_variant ; 4546.0bp to feature; MODIFIER silent_mutation Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0722812632 C -> T LOC_Os07g38040-LOC_Os07g38050 intergenic_region ; MODIFIER silent_mutation Average:67.205; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0722812632 NA 7.56E-09 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
vg0722812632 1.07E-06 6.15E-07 mr1758_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
vg0722812632 NA 1.14E-08 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
vg0722812632 NA 8.66E-07 mr1842_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