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

Detailed information for vg1012239875:

Variant ID: vg1012239875 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 12239875
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTCGCATAAGGCCTGGTCGAATTGCTGTGCCCCAATCGAGCAGGTGATCGTGGGACACCCCGGATCTTTCTTCTTTTCCGGGAGTTTGTGGAGTATGAC[A/G]
TTGCTGCATTGTAACGTCAGCTTGACCACCTCCGTTGTTGGGAGTGGTCTCTTGTTGTTGAGTATGTCCTTCAGATAACAGGCGTATGTCGGCACTTGCA

Reverse complement sequence

TGCAAGTGCCGACATACGCCTGTTATCTGAAGGACATACTCAACAACAAGAGACCACTCCCAACAACGGAGGTGGTCAAGCTGACGTTACAATGCAGCAA[T/C]
GTCATACTCCACAAACTCCCGGAAAAGAAGAAAGATCCGGGGTGTCCCACGATCACCTGCTCGATTGGGGCACAGCAATTCGACCAGGCCTTATGCGACC

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 31.80% 17.90% 0.70% 49.56% NA
All Indica  2759 3.70% 28.70% 0.98% 66.65% NA
All Japonica  1512 89.40% 0.50% 0.33% 9.79% NA
Aus  269 1.90% 9.70% 0.37% 88.10% NA
Indica I  595 6.70% 7.40% 1.68% 84.20% NA
Indica II  465 3.90% 36.10% 0.65% 59.35% NA
Indica III  913 1.20% 33.70% 0.66% 64.40% NA
Indica Intermediate  786 4.10% 34.60% 1.02% 60.31% NA
Temperate Japonica  767 97.10% 0.30% 0.13% 2.48% NA
Tropical Japonica  504 82.10% 0.40% 0.60% 16.87% NA
Japonica Intermediate  241 80.10% 1.20% 0.41% 18.26% NA
VI/Aromatic  96 8.30% 4.20% 0.00% 87.50% NA
Intermediate  90 42.20% 20.00% 0.00% 37.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1012239875 A -> G LOC_Os10g23870.1 synonymous_variant ; p.Asn101Asn; LOW synonymous_codon Average:10.968; most accessible tissue: Callus, score: 25.765 N N N N
vg1012239875 A -> DEL LOC_Os10g23870.1 N frameshift_variant Average:10.968; most accessible tissue: Callus, score: 25.765 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1012239875 NA 9.01E-08 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
vg1012239875 NA 3.60E-06 mr1157 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
vg1012239875 9.81E-07 5.74E-10 mr1328 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
vg1012239875 2.23E-06 1.36E-08 mr1328 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
vg1012239875 1.24E-06 1.30E-10 mr1446 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
vg1012239875 3.86E-07 5.15E-09 mr1446 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
vg1012239875 NA 5.21E-07 mr1236_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
vg1012239875 NA 9.05E-06 mr1419_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
vg1012239875 NA 3.55E-10 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
vg1012239875 NA 3.42E-07 mr1446_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
vg1012239875 NA 4.26E-07 mr1706_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