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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1009652919:

Variant ID: vg1009652919 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9652919
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.37, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


TGACCGTCTTTTGCAGAATATTCTTGATTTATTTGTTTGATGTTTCTTCTTGTCCACTGGTCTGTGGATGGTAAGGAGTAGCCACATTGTGTTTGGCTCC[C/T]
ATTTCTCGTAGGAGGTCTCGGAAGGTTTTATCAATGAAATGAGAACCTCCGTCACTTATGACCATTCTGGGGGTACCAAATCTTGGGAAGATGATTTCTG

Reverse complement sequence

CAGAAATCATCTTCCCAAGATTTGGTACCCCCAGAATGGTCATAAGTGACGGAGGTTCTCATTTCATTGATAAAACCTTCCGAGACCTCCTACGAGAAAT[G/A]
GGAGCCAAACACAATGTGGCTACTCCTTACCATCCACAGACCAGTGGACAAGAAGAAACATCAAACAAATAAATCAAGAATATTCTGCAAAAGACGGTCA

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 45.90% 41.90% 2.77% 9.42% NA
All Indica  2759 25.00% 56.20% 4.35% 14.46% NA
All Japonica  1512 73.70% 23.30% 0.53% 2.51% NA
Aus  269 87.70% 11.50% 0.74% 0.00% NA
Indica I  595 12.80% 72.30% 3.03% 11.93% NA
Indica II  465 35.50% 40.20% 5.16% 19.14% NA
Indica III  913 22.50% 60.80% 5.04% 11.72% NA
Indica Intermediate  786 30.90% 48.20% 4.07% 16.79% NA
Temperate Japonica  767 83.10% 16.60% 0.13% 0.26% NA
Tropical Japonica  504 70.00% 21.80% 1.39% 6.75% NA
Japonica Intermediate  241 51.50% 47.70% 0.00% 0.83% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 58.90% 31.10% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009652919 C -> T LOC_Os10g18960.1 missense_variant ; p.Met337Ile; MODERATE nonsynonymous_codon ; M337I Average:42.697; most accessible tissue: Minghui63 flag leaf, score: 63.692 benign 0.376 DELETERIOUS 0.05
vg1009652919 C -> DEL LOC_Os10g18960.1 N frameshift_variant Average:42.697; most accessible tissue: Minghui63 flag leaf, score: 63.692 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009652919 7.46E-06 7.45E-06 mr1027 Ind_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
vg1009652919 NA 4.18E-06 mr1053 Ind_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
vg1009652919 3.68E-06 NA mr1070 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
vg1009652919 NA 3.10E-06 mr1128 Ind_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
vg1009652919 NA 2.42E-06 mr1405 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
vg1009652919 2.00E-07 1.29E-12 mr1709 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
vg1009652919 1.14E-06 2.00E-14 mr1709 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
vg1009652919 NA 8.61E-06 mr1772 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
vg1009652919 NA 5.70E-06 mr1792 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
vg1009652919 NA 1.09E-08 mr1027_2 Ind_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
vg1009652919 NA 1.03E-15 mr1709_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
vg1009652919 NA 8.50E-14 mr1709_2 Ind_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