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Detailed information for vg1009664258:

Variant ID: vg1009664258 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9664258
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


AATGCGATCCAAAATCGTTTTTCCTTGTGACGGCATTTTGTGTATGAATGATCCTCCAGCGGTTATGTCCAAATAGAATGCAGACTCCTTATCCAAACTC[G/A]
TATGGAAATGTGGGAGAAGCACATACTCGGGTAAGGACAGGGTTGGTCCGGACTGGACTAAATTAGTGAATCTGGACCAAGCTGCACCGATTGATTCGTT

Reverse complement sequence

AACGAATCAATCGGTGCAGCTTGGTCCAGATTCACTAATTTAGTCCAGTCCGGACCAACCCTGTCCTTACCCGAGTATGTGCTTCTCCCACATTTCCATA[C/T]
GAGTTTGGATAAGGAGTCTGCATTCTATTTGGACATAACCGCTGGAGGATCATTCATACACAAAATGCCGTCACAAGGAAAAACGATTTTGGATCGCATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.50% 19.20% 5.76% 17.54% NA
All Indica  2759 37.40% 25.50% 9.46% 27.65% NA
All Japonica  1512 83.50% 12.80% 0.26% 3.44% NA
Aus  269 98.50% 0.00% 0.37% 1.12% NA
Indica I  595 74.30% 1.80% 1.68% 22.18% NA
Indica II  465 19.40% 24.50% 18.49% 37.63% NA
Indica III  913 21.90% 45.10% 9.20% 23.77% NA
Indica Intermediate  786 38.20% 21.10% 10.31% 30.41% NA
Temperate Japonica  767 94.90% 4.80% 0.00% 0.26% NA
Tropical Japonica  504 70.20% 19.80% 0.79% 9.13% NA
Japonica Intermediate  241 74.70% 23.70% 0.00% 1.66% NA
VI/Aromatic  96 96.90% 0.00% 2.08% 1.04% NA
Intermediate  90 71.10% 13.30% 4.44% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009664258 G -> A LOC_Os10g18980.1 missense_variant ; p.Thr65Met; MODERATE nonsynonymous_codon ; T65M Average:41.027; most accessible tissue: Minghui63 young leaf, score: 65.161 benign 0.786 TOLERATED 0.06
vg1009664258 G -> DEL LOC_Os10g18980.1 N frameshift_variant Average:41.027; most accessible tissue: Minghui63 young leaf, score: 65.161 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009664258 NA 4.19E-11 mr1113 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
vg1009664258 5.08E-06 4.70E-09 mr1114 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
vg1009664258 NA 1.88E-07 mr1116 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
vg1009664258 NA 6.05E-13 mr1118 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
vg1009664258 NA 4.09E-06 mr1119 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
vg1009664258 7.46E-07 NA mr1120 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
vg1009664258 9.25E-09 2.28E-11 mr1120 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
vg1009664258 NA 4.54E-07 mr1183 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
vg1009664258 NA 9.31E-07 mr1247 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
vg1009664258 7.97E-06 5.93E-18 mr1495 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
vg1009664258 NA 3.65E-06 mr1495 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
vg1009664258 NA 8.64E-07 mr1503 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
vg1009664258 NA 4.02E-13 mr1794 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
vg1009664258 NA 2.00E-09 mr1794 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
vg1009664258 NA 3.07E-07 mr1917 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
vg1009664258 NA 8.38E-09 mr1113_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
vg1009664258 NA 1.13E-10 mr1114_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
vg1009664258 NA 6.39E-08 mr1117_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
vg1009664258 NA 1.53E-13 mr1118_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
vg1009664258 NA 4.34E-06 mr1118_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
vg1009664258 NA 7.57E-07 mr1119_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
vg1009664258 NA 1.59E-09 mr1120_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
vg1009664258 NA 6.31E-09 mr1247_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
vg1009664258 NA 9.70E-16 mr1495_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
vg1009664258 NA 1.84E-07 mr1495_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
vg1009664258 NA 7.35E-17 mr1794_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