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Detailed information for vg1004500188:

Variant ID: vg1004500188 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4500188
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTATGGTAGGTACGTGCTTTTTTTTTCCTCATAATAGTTATATGTAACCTTTTTTCTCATTTTACATACGTACTTATGTTTTTTTGTTCTTTGACCATC[G/A]
AGGTGCATACAGATCTACTAAGCACGCTATGTTTTATTTTAGCTTTTGTCGTACATACAGGAGAAAGGTATTATATATATAGAGAGATCTGATTTATTGT

Reverse complement sequence

ACAATAAATCAGATCTCTCTATATATATAATACCTTTCTCCTGTATGTACGACAAAAGCTAAAATAAAACATAGCGTGCTTAGTAGATCTGTATGCACCT[C/T]
GATGGTCAAAGAACAAAAAAACATAAGTACGTATGTAAAATGAGAAAAAAGGTTACATATAACTATTATGAGGAAAAAAAAAGCACGTACCTACCATAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.70% 15.30% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 55.50% 44.50% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 26.70% 73.30% 0.00% 0.00% NA
Tropical Japonica  504 95.00% 5.00% 0.00% 0.00% NA
Japonica Intermediate  241 64.30% 35.70% 0.00% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 86.70% 13.30% 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
vg1004500188 G -> A LOC_Os10g08319.1 intron_variant ; MODIFIER silent_mutation Average:33.705; most accessible tissue: Callus, score: 62.945 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004500188 NA 2.89E-07 mr1118 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
vg1004500188 NA 7.17E-06 mr1495 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
vg1004500188 NA 6.08E-06 mr1892 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
vg1004500188 NA 1.35E-07 mr1261_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
vg1004500188 NA 9.52E-08 mr1563_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
vg1004500188 NA 1.43E-07 mr1606_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
vg1004500188 1.94E-06 9.94E-32 mr1768_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
vg1004500188 NA 4.34E-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