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Detailed information for vg1100083618:

Variant ID: vg1100083618 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 83618
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGTTTGGTTAGGGAGAGAGAGAGTGGCGATAATTATAAGGGACAATTGTTTATTTGACTTTGTTTTGAAGCCTAACTACCAATTTGACTCTATTTTTT[C/T]
TAGTTTGCTTATTTGCCTGCTTTTCGAAAATGAACACTCCGTCTGACCTGTTTCTACAACACCGTTAAGAGTTCATTTTAAAAAAGAGGAAAAATAAAAA

Reverse complement sequence

TTTTTATTTTTCCTCTTTTTTAAAATGAACTCTTAACGGTGTTGTAGAAACAGGTCAGACGGAGTGTTCATTTTCGAAAAGCAGGCAAATAAGCAAACTA[G/A]
AAAAAATAGAGTCAAATTGGTAGTTAGGCTTCAAAACAAAGTCAAATAAACAATTGTCCCTTATAATTATCGCCACTCTCTCTCTCCCTAACCAAACACC

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 93.50% 2.10% 4.34% 0.06% NA
All Indica  2759 89.40% 3.60% 7.07% 0.00% NA
All Japonica  1512 99.10% 0.10% 0.53% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.40% 3.00% 8.57% 0.00% NA
Indica II  465 98.10% 0.20% 1.72% 0.00% NA
Indica III  913 86.00% 4.90% 9.09% 0.00% NA
Indica Intermediate  786 88.90% 4.30% 6.74% 0.00% NA
Temperate Japonica  767 98.30% 0.30% 1.04% 0.39% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 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
vg1100083618 C -> T LOC_Os11g01140.1 intron_variant ; MODIFIER silent_mutation Average:27.257; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1100083618 C -> T LOC_Os11g01140.2 intron_variant ; MODIFIER silent_mutation Average:27.257; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1100083618 C -> T LOC_Os11g01140.3 intron_variant ; MODIFIER silent_mutation Average:27.257; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg1100083618 C -> DEL N N silent_mutation Average:27.257; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100083618 NA 9.89E-07 mr1291 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
vg1100083618 NA 1.31E-08 mr1291 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
vg1100083618 NA 5.10E-06 mr1502 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
vg1100083618 NA 7.85E-06 mr1502 Ind_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
vg1100083618 NA 4.90E-06 mr1892 Ind_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
vg1100083618 NA 1.85E-07 mr1543_2 Ind_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