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Detailed information for vg1001398311:

Variant ID: vg1001398311 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1398311
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCTAACTGAGATGGTGAATGCCATGTTAGACATTGCGGGGCTTTCCAAGGAATGGTGGGTTGAGGCAGTTTTGATTGCGTGTCATGTCCTGAATAAAAT[G/T]
CCAATGAAGCATAAGGAAGTAACACCATTCGAGGAATGGGAAAGGAAGAAATTAAATCTCTCATACCTACGAACATGGGGCTGTTTGGCCAAGGTAAATG

Reverse complement sequence

CATTTACCTTGGCCAAACAGCCCCATGTTCGTAGGTATGAGAGATTTAATTTCTTCCTTTCCCATTCCTCGAATGGTGTTACTTCCTTATGCTTCATTGG[C/A]
ATTTTATTCAGGACATGACACGCAATCAAAACTGCCTCAACCCACCATTCCTTGGAAAGCCCCGCAATGTCTAACATGGCATTCACCATCTCAGTTAGAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 13.60% 9.30% 52.37% 24.74% NA
All Indica  2759 1.20% 15.20% 44.55% 39.07% NA
All Japonica  1512 38.80% 0.40% 56.48% 4.30% NA
Aus  269 2.60% 0.00% 94.05% 3.35% NA
Indica I  595 2.40% 0.20% 38.15% 59.33% NA
Indica II  465 1.10% 30.80% 34.84% 33.33% NA
Indica III  913 0.50% 19.90% 50.38% 29.13% NA
Indica Intermediate  786 1.00% 12.00% 48.35% 38.68% NA
Temperate Japonica  767 71.10% 0.40% 25.68% 2.87% NA
Tropical Japonica  504 2.20% 0.40% 91.87% 5.56% NA
Japonica Intermediate  241 12.90% 0.40% 80.50% 6.22% NA
VI/Aromatic  96 3.10% 0.00% 90.62% 6.25% NA
Intermediate  90 14.40% 15.60% 57.78% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001398311 G -> T LOC_Os10g03300.1 missense_variant ; p.Met720Ile; MODERATE nonsynonymous_codon ; M720I Average:10.944; most accessible tissue: Callus, score: 20.558 probably damaging -2.179 TOLERATED 0.94
vg1001398311 G -> DEL LOC_Os10g03300.1 N frameshift_variant Average:10.944; most accessible tissue: Callus, score: 20.558 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001398311 NA 1.30E-06 mr1026 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
vg1001398311 NA 3.30E-07 mr1063 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
vg1001398311 NA 3.62E-07 mr1206 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
vg1001398311 8.37E-07 7.44E-25 mr1300 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
vg1001398311 NA 1.51E-35 mr1310 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
vg1001398311 NA 1.00E-06 mr1310 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
vg1001398311 1.88E-06 4.45E-40 mr1486 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
vg1001398311 5.42E-06 3.64E-15 mr1486 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
vg1001398311 7.83E-06 6.10E-10 mr1548 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
vg1001398311 NA 9.54E-09 mr1570 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
vg1001398311 NA 4.82E-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
vg1001398311 NA 1.33E-06 mr1668 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
vg1001398311 5.97E-07 3.01E-42 mr1926 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
vg1001398311 NA 6.95E-13 mr1959 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
vg1001398311 NA 3.50E-06 mr1063_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
vg1001398311 NA 2.92E-06 mr1161_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
vg1001398311 2.12E-06 3.17E-37 mr1310_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
vg1001398311 NA 7.33E-10 mr1310_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
vg1001398311 2.13E-14 1.11E-53 mr1486_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
vg1001398311 1.33E-11 1.21E-19 mr1486_2 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
vg1001398311 NA 4.34E-06 mr1588_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
vg1001398311 NA 9.93E-17 mr1959_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
vg1001398311 NA 3.41E-06 mr1959_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