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Detailed information for vg1011365856:

Variant ID: vg1011365856 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 11365856
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGCTGCTTGGCACTCTGGTGTCCAATTAAACTTTCCTGCGCCCCGGAGGGTCTTCAAGAAGGGCAAACCTCTTTCGGCTGCCTTTGAGAGGAATCGACT[A/G]
AGTGCTGCAATTCAGCCTGCAAGCTTTTGTACTTCATGTACGCTTGACGGAGGCTTCATTTGCTGGATGGCATCGATTTTCTCGGGATTCGCCTCGATGC

Reverse complement sequence

GCATCGAGGCGAATCCCGAGAAAATCGATGCCATCCAGCAAATGAAGCCTCCGTCAAGCGTACATGAAGTACAAAAGCTTGCAGGCTGAATTGCAGCACT[T/C]
AGTCGATTCCTCTCAAAGGCAGCCGAAAGAGGTTTGCCCTTCTTGAAGACCCTCCGGGGCGCAGGAAAGTTTAATTGGACACCAGAGTGCCAAGCAGCAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 27.40% 0.80% 40.41% 31.38% NA
All Indica  2759 15.50% 1.20% 65.42% 17.87% NA
All Japonica  1512 37.50% 0.10% 2.58% 59.85% NA
Aus  269 86.20% 0.70% 5.58% 7.43% NA
Indica I  595 5.90% 1.00% 66.55% 26.55% NA
Indica II  465 15.30% 0.40% 69.89% 14.41% NA
Indica III  913 17.20% 1.90% 71.63% 9.31% NA
Indica Intermediate  786 20.90% 1.10% 54.71% 23.28% NA
Temperate Japonica  767 68.70% 0.00% 2.09% 29.20% NA
Tropical Japonica  504 1.60% 0.20% 2.58% 95.63% NA
Japonica Intermediate  241 13.30% 0.00% 4.15% 82.57% NA
VI/Aromatic  96 37.50% 0.00% 18.75% 43.75% NA
Intermediate  90 36.70% 1.10% 36.67% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1011365856 A -> G LOC_Os10g22000.1 downstream_gene_variant ; 2859.0bp to feature; MODIFIER silent_mutation Average:9.875; most accessible tissue: Minghui63 root, score: 17.665 N N N N
vg1011365856 A -> G LOC_Os10g22010.1 intron_variant ; MODIFIER silent_mutation Average:9.875; most accessible tissue: Minghui63 root, score: 17.665 N N N N
vg1011365856 A -> DEL N N silent_mutation Average:9.875; most accessible tissue: Minghui63 root, score: 17.665 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011365856 NA 8.52E-07 mr1157 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
vg1011365856 NA 6.02E-06 mr1192 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
vg1011365856 NA 3.45E-08 mr1627 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
vg1011365856 NA 3.02E-08 mr1826 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
vg1011365856 NA 8.30E-06 mr1112_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
vg1011365856 NA 6.75E-06 mr1194_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
vg1011365856 NA 1.61E-07 mr1206_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
vg1011365856 NA 1.67E-06 mr1211_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
vg1011365856 NA 4.05E-09 mr1229_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
vg1011365856 NA 5.82E-06 mr1246_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
vg1011365856 NA 1.66E-06 mr1250_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
vg1011365856 NA 2.93E-07 mr1263_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
vg1011365856 NA 2.79E-07 mr1446_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
vg1011365856 NA 1.38E-09 mr1486_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
vg1011365856 NA 9.81E-09 mr1521_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
vg1011365856 NA 2.50E-09 mr1570_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
vg1011365856 NA 9.97E-07 mr1596_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
vg1011365856 NA 9.44E-12 mr1611_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
vg1011365856 NA 1.48E-07 mr1617_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
vg1011365856 NA 2.23E-06 mr1693_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
vg1011365856 NA 8.42E-07 mr1763_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
vg1011365856 NA 1.90E-06 mr1763_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
vg1011365856 NA 6.67E-06 mr1844_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
vg1011365856 NA 2.48E-08 mr1880_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