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Detailed information for vg1008819475:

Variant ID: vg1008819475 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 8819475
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATATTTTTGTAAGACGTGGGTCTGTATGTCAACAATTGTCGTTTGTGTACCTTGGCAGGTCCTGGACAGGGATTTAATGCACATTCAGCTTAGAAATT[C/A]
TGATTCGAGAATTTCTGGGTGTGACAAGTTGGTATCAGAGCCGACCTTGACCGTAGGACAAGCCAACTGGAAACCTAAGAGCCCTCTGAACCCTTTTTTT

Reverse complement sequence

AAAAAAAGGGTTCAGAGGGCTCTTAGGTTTCCAGTTGGCTTGTCCTACGGTCAAGGTCGGCTCTGATACCAACTTGTCACACCCAGAAATTCTCGAATCA[G/T]
AATTTCTAAGCTGAATGTGCATTAAATCCCTGTCCAGGACCTGCCAAGGTACACAAACGACAATTGTTGACATACAGACCCACGTCTTACAAAAATATAA

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 65.00% 13.10% 0.40% 21.56% NA
All Indica  2759 95.50% 1.00% 0.25% 3.23% NA
All Japonica  1512 23.70% 38.10% 0.33% 37.90% NA
Aus  269 1.90% 0.40% 1.49% 96.28% NA
Indica I  595 98.00% 0.50% 0.00% 1.51% NA
Indica II  465 97.80% 1.10% 0.22% 0.86% NA
Indica III  913 95.20% 0.70% 0.33% 3.83% NA
Indica Intermediate  786 92.60% 1.80% 0.38% 5.22% NA
Temperate Japonica  767 6.40% 53.10% 0.13% 40.42% NA
Tropical Japonica  504 46.40% 8.30% 0.40% 44.84% NA
Japonica Intermediate  241 31.10% 52.70% 0.83% 15.35% NA
VI/Aromatic  96 25.00% 0.00% 3.12% 71.88% NA
Intermediate  90 53.30% 14.40% 0.00% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1008819475 C -> A LOC_Os10g17489.1 intron_variant ; MODIFIER silent_mutation Average:23.128; most accessible tissue: Minghui63 root, score: 54.099 N N N N
vg1008819475 C -> DEL N N silent_mutation Average:23.128; most accessible tissue: Minghui63 root, score: 54.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1008819475 NA 1.56E-07 mr1157 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
vg1008819475 NA 1.11E-08 mr1446 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
vg1008819475 NA 3.45E-09 mr1709_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
vg1008819475 NA 2.09E-07 mr1768_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
vg1008819475 NA 9.91E-06 mr1942_2 Ind_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