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Detailed information for vg1001395986:

Variant ID: vg1001395986 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1395986
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTGTGGGGAGTGCTTCTCGCACGACTGCTCGTCCTCGTCCACCATGTCTACGCCTGGAGCCGGAGCTGCCGCCGGCGCCGCCGCCGCTGCTGCTGCT[A/G]
GAGGAGATGGCGCGCCTGGAGCTGGAGCCGGAGATGGCACGCCTGGAGCCGGTGCCGCGAACGTCAACACCAAGGGAGGCAATTCTGCCTCACAATCCAG

Reverse complement sequence

CTGGATTGTGAGGCAGAATTGCCTCCCTTGGTGTTGACGTTCGCGGCACCGGCTCCAGGCGTGCCATCTCCGGCTCCAGCTCCAGGCGCGCCATCTCCTC[T/C]
AGCAGCAGCAGCGGCGGCGGCGCCGGCGGCAGCTCCGGCTCCAGGCGTAGACATGGTGGACGAGGACGAGCAGTCGTGCGAGAAGCACTCCCCACAAACC

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 85.30% 2.40% 4.80% 7.58% NA
All Indica  2759 95.80% 0.80% 1.01% 2.36% NA
All Japonica  1512 69.40% 4.20% 9.85% 16.53% NA
Aus  269 97.40% 1.50% 1.12% 0.00% NA
Indica I  595 98.20% 0.20% 0.67% 1.01% NA
Indica II  465 96.10% 0.90% 0.65% 2.37% NA
Indica III  913 95.80% 0.50% 0.88% 2.74% NA
Indica Intermediate  786 93.90% 1.50% 1.65% 2.93% NA
Temperate Japonica  767 74.80% 2.10% 7.30% 15.78% NA
Tropical Japonica  504 78.40% 4.40% 7.74% 9.52% NA
Japonica Intermediate  241 33.20% 10.80% 22.41% 33.61% NA
VI/Aromatic  96 9.40% 13.50% 41.67% 35.42% NA
Intermediate  90 72.20% 10.00% 7.78% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001395986 A -> G LOC_Os10g03300.1 missense_variant ; p.Arg19Gly; MODERATE nonsynonymous_codon ; R19G Average:54.933; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 unknown unknown TOLERATED 1.00
vg1001395986 A -> DEL LOC_Os10g03300.1 N frameshift_variant Average:54.933; most accessible tissue: Zhenshan97 flag leaf, score: 79.006 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001395986 3.66E-06 7.19E-07 mr1304 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
vg1001395986 6.83E-11 1.28E-41 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
vg1001395986 3.40E-09 3.80E-30 mr1548 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
vg1001395986 NA 5.20E-07 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
vg1001395986 5.19E-06 5.55E-07 mr1685 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
vg1001395986 5.85E-15 2.73E-52 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
vg1001395986 3.23E-06 NA mr1486_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
vg1001395986 2.91E-07 NA 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