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Detailed information for vg0729570786:

Variant ID: vg0729570786 (JBrowse)Variation Type: INDEL
Chromosome: chr07Position: 29570786
Reference Allele: CCATAACATAlternative Allele: TCATAACAT,C
Primary Allele: CCATAACATSecondary Allele: TCATAACAT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGATGAGCGGACTCGTCGGACTTTTAACTGTAGCTCATGATTTTCTAGAAATATATAGATTCAAGTGAATTCACATAGTGAATTTCATCTTAACTAAA[CCATAACAT/TCATAACAT,C]
GTTACAACGTACGAGTATTTTTTTCTAAGACTCTAATAAGGATGTAGTGTACGCATATACGTAGGTATGTATTGTGATGCTGTACCTGATGTCCCTGAGG

Reverse complement sequence

CCTCAGGGACATCAGGTACAGCATCACAATACATACCTACGTATATGCGTACACTACATCCTTATTAGAGTCTTAGAAAAAAATACTCGTACGTTGTAAC[ATGTTATGG/ATGTTATGA,G]
TTTAGTTAAGATGAAATTCACTATGTGAATTCACTTGAATCTATATATTTCTAGAAAATCATGAGCTACAGTTAAAAGTCCGACGAGTCCGCTCATCACA

Allele Frequencies:

Populations Population SizeFrequency of CCATAACAT(primary allele) Frequency of TCATAACAT(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.60% 2.50% 0.83% 0.00% C: 0.02%
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.80% 7.70% 2.51% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 80.40% 14.60% 4.95% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 0.00% C: 1.04%
Intermediate  90 95.60% 3.30% 1.11% 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
vg0729570786 CCATAACAT -> TCATAACAT LOC_Os07g49370.1 intron_variant ; MODIFIER silent_mutation Average:67.119; most accessible tissue: Callus, score: 89.257 N N N N
vg0729570786 CCATAACAT -> C LOC_Os07g49370.1 intron_variant ; MODIFIER silent_mutation Average:67.119; most accessible tissue: Callus, score: 89.257 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0729570786 NA 1.91E-07 mr1354 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
vg0729570786 NA 2.72E-06 mr1902 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
vg0729570786 NA 3.65E-08 mr1354_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
vg0729570786 NA 1.05E-06 mr1576_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
vg0729570786 7.77E-07 9.99E-06 mr1666_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
vg0729570786 NA 1.03E-07 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
vg0729570786 NA 6.04E-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
vg0729570786 NA 8.70E-07 mr1902_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