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Detailed information for vg0419753293:

Variant ID: vg0419753293 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19753293
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCACCGGTGCGGTAGTTCACCTACAAAAGAAGATCAAGCTCTTTTAGGTACCTAAACTTGTTTGGGTCCTTGGAGGTTAGAGTCCAAAGCTTTGGGCA[T/C]
CCAAATGGCATTCTTTTTACCACCGAGTATAGGGGAACCCACATATCTAGCAACAATACTACCATCATAAGCCTTCCTAAGCATATAATGAGAATCGAAC

Reverse complement sequence

GTTCGATTCTCATTATATGCTTAGGAAGGCTTATGATGGTAGTATTGTTGCTAGATATGTGGGTTCCCCTATACTCGGTGGTAAAAAGAATGCCATTTGG[A/G]
TGCCCAAAGCTTTGGACTCTAACCTCCAAGGACCCAAACAAGTTTAGGTACCTAAAAGAGCTTGATCTTCTTTTGTAGGTGAACTACCGCACCGGTGGGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 41.50% 7.20% 2.43% 48.94% NA
All Indica  2759 7.90% 8.70% 2.50% 80.97% NA
All Japonica  1512 99.70% 0.00% 0.07% 0.26% NA
Aus  269 34.90% 32.00% 12.27% 20.82% NA
Indica I  595 14.30% 0.00% 0.67% 85.04% NA
Indica II  465 7.30% 7.10% 1.94% 83.66% NA
Indica III  913 3.80% 15.00% 4.27% 76.89% NA
Indica Intermediate  786 8.00% 8.80% 2.16% 81.04% NA
Temperate Japonica  767 99.60% 0.00% 0.13% 0.26% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 12.50% 11.46% 6.25% NA
Intermediate  90 83.30% 1.10% 1.11% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419753293 T -> C LOC_Os04g32750.1 intron_variant ; MODIFIER silent_mutation Average:5.79; most accessible tissue: Callus, score: 16.05 N N N N
vg0419753293 T -> DEL N N silent_mutation Average:5.79; most accessible tissue: Callus, score: 16.05 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0419753293 3.80E-06 8.00E-08 mr1587 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
vg0419753293 NA 1.09E-19 mr1588 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
vg0419753293 NA 2.58E-11 mr1713 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
vg0419753293 NA 2.77E-07 mr1321_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
vg0419753293 NA 1.80E-07 mr1568_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
vg0419753293 NA 3.48E-20 mr1581_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
vg0419753293 NA 3.05E-24 mr1588_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
vg0419753293 NA 2.14E-12 mr1666_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
vg0419753293 NA 8.16E-13 mr1713_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
vg0419753293 NA 1.24E-12 mr1717_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
vg0419753293 NA 1.83E-51 mr1721_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
vg0419753293 NA 6.46E-11 mr1761_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
vg0419753293 NA 2.89E-14 mr1938_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