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Detailed information for vg0801634535:

Variant ID: vg0801634535 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 1634535
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTATATAAATTCCTCCATGGTCATCAGCTCGATCGGTCACTCTCAGCAAGCTCGATCAGATTCAGAGATGGCATCGTCTCGCCCCATCTCGGAGAGCAC[C/T]
ATCACGAGGTCGACGTGCGCGACGCGGACGGCGCGCGCCACGCACCAGTTCGAGATCGTCGGGTACAGCCTCAAGAGGTGCCTCGCCGCCGGCGAGTTCG

Reverse complement sequence

CGAACTCGCCGGCGGCGAGGCACCTCTTGAGGCTGTACCCGACGATCTCGAACTGGTGCGTGGCGCGCGCCGTCCGCGTCGCGCACGTCGACCTCGTGAT[G/A]
GTGCTCTCCGAGATGGGGCGAGACGATGCCATCTCTGAATCTGATCGAGCTTGCTGAGAGTGACCGATCGAGCTGATGACCATGGAGGAATTTATATACT

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 93.90% 5.40% 0.00% 0.70% NA
All Indica  2759 97.70% 1.10% 0.00% 1.20% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 19.30% 80.70% 0.00% 0.00% NA
Indica I  595 97.60% 0.00% 0.00% 2.35% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.40% 0.90% 0.00% 0.77% NA
Indica Intermediate  786 95.70% 2.80% 0.00% 1.53% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0801634535 C -> T LOC_Os08g03490.1 synonymous_variant ; p.Thr11Thr; LOW synonymous_codon Average:71.41; most accessible tissue: Minghui63 root, score: 77.29 N N N N
vg0801634535 C -> DEL LOC_Os08g03490.1 N frameshift_variant Average:71.41; most accessible tissue: Minghui63 root, score: 77.29 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0801634535 NA 7.05E-06 mr1230 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
vg0801634535 NA 2.44E-18 mr1515 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
vg0801634535 NA 7.85E-06 mr1633 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
vg0801634535 NA 4.66E-06 mr1344_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
vg0801634535 NA 1.14E-07 mr1510_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
vg0801634535 NA 1.45E-15 mr1587_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
vg0801634535 NA 8.76E-13 mr1803_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