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Detailed information for vg1001593604:

Variant ID: vg1001593604 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1593604
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGGTTGACCAGATTTACCGTGATTAGTCCCACCTTAATAAATTGACTCAATGCACTGTAGTTCAGGTGGGTTGGTTGGGCCTGTTCAACGTGGTGTAG[C/T]
GTTGATCAGTGGAGATTTAATGTTACTTTAATTACTCAACAGTTTAACCGTTTTGCTCAATAAAATGTTTTACAACCGCCTTTATGCAAATAGCCACAAA

Reverse complement sequence

TTTGTGGCTATTTGCATAAAGGCGGTTGTAAAACATTTTATTGAGCAAAACGGTTAAACTGTTGAGTAATTAAAGTAACATTAAATCTCCACTGATCAAC[G/A]
CTACACCACGTTGAACAGGCCCAACCAACCCACCTGAACTACAGTGCATTGAGTCAATTTATTAAGGTGGGACTAATCACGGTAAATCTGGTCAACCGCC

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 71.30% 16.90% 6.43% 5.33% NA
All Indica  2759 84.00% 2.10% 7.65% 6.31% NA
All Japonica  1512 55.00% 41.60% 0.93% 2.51% NA
Aus  269 60.20% 0.40% 27.14% 12.27% NA
Indica I  595 90.90% 0.20% 7.73% 1.18% NA
Indica II  465 87.70% 2.60% 5.81% 3.87% NA
Indica III  913 79.30% 1.90% 8.11% 10.73% NA
Indica Intermediate  786 81.90% 3.40% 8.14% 6.49% NA
Temperate Japonica  767 78.70% 20.70% 0.39% 0.13% NA
Tropical Japonica  504 21.40% 69.60% 1.59% 7.34% NA
Japonica Intermediate  241 49.40% 49.40% 1.24% 0.00% NA
VI/Aromatic  96 10.40% 87.50% 2.08% 0.00% NA
Intermediate  90 54.40% 33.30% 4.44% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001593604 C -> T LOC_Os10g03640.1 upstream_gene_variant ; 3107.0bp to feature; MODIFIER silent_mutation Average:27.902; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N
vg1001593604 C -> T LOC_Os10g03640-LOC_Os10g03660 intergenic_region ; MODIFIER silent_mutation Average:27.902; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N
vg1001593604 C -> DEL N N silent_mutation Average:27.902; most accessible tissue: Zhenshan97 flag leaf, score: 61.322 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001593604 NA 4.25E-15 mr1118 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
vg1001593604 NA 3.41E-06 mr1192 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
vg1001593604 NA 2.70E-12 mr1205 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
vg1001593604 NA 1.92E-08 mr1206 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
vg1001593604 NA 2.14E-06 mr1209 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
vg1001593604 NA 1.26E-08 mr1236 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
vg1001593604 NA 2.64E-07 mr1278 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
vg1001593604 NA 7.29E-09 mr1332 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
vg1001593604 NA 1.05E-06 mr1338 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
vg1001593604 NA 2.40E-08 mr1570 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
vg1001593604 NA 5.10E-06 mr1596 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
vg1001593604 NA 7.80E-06 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