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

Detailed information for vg1223453821:

Variant ID: vg1223453821 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23453821
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTTAGAGAGATAATTCCACACGCTGGTCCTCGAACCAGCAAACCCGTAGCAATCTCTCACACCGCGACTTCCATTGGTGCTAGAGAGATAATTCTACG[C/T]
GCTGGTTCTCGAACCAGTAAACCCGTAGCAATCGCTCACACCGTGACTTCCATTGGTGCTAGAGAGATAATTCTATGCGCTGGTCCTCGAACCAGCAAAC

Reverse complement sequence

GTTTGCTGGTTCGAGGACCAGCGCATAGAATTATCTCTCTAGCACCAATGGAAGTCACGGTGTGAGCGATTGCTACGGGTTTACTGGTTCGAGAACCAGC[G/A]
CGTAGAATTATCTCTCTAGCACCAATGGAAGTCGCGGTGTGAGAGATTGCTACGGGTTTGCTGGTTCGAGGACCAGCGTGTGGAATTATCTCTCTAACAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.30% 28.90% 3.39% 5.35% NA
All Indica  2759 87.50% 2.80% 0.80% 8.92% NA
All Japonica  1512 18.90% 72.40% 8.33% 0.40% NA
Aus  269 69.10% 27.90% 2.97% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 58.70% 4.30% 2.15% 34.84% NA
Indica III  913 97.40% 1.50% 0.00% 1.10% NA
Indica Intermediate  786 85.50% 3.60% 1.53% 9.41% NA
Temperate Japonica  767 31.80% 55.90% 11.47% 0.78% NA
Tropical Japonica  504 2.60% 93.80% 3.57% 0.00% NA
Japonica Intermediate  241 12.00% 79.70% 8.30% 0.00% NA
VI/Aromatic  96 11.50% 87.50% 0.00% 1.04% NA
Intermediate  90 54.40% 41.10% 4.44% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1223453821 C -> DEL LOC_Os12g38190.1 N frameshift_variant Average:23.608; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 N N N N
vg1223453821 C -> T LOC_Os12g38190.1 synonymous_variant ; p.Arg307Arg; LOW synonymous_codon Average:23.608; most accessible tissue: Zhenshan97 flag leaf, score: 38.066 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223453821 NA 3.90E-06 mr1002 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
vg1223453821 NA 2.98E-08 mr1130 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
vg1223453821 NA 2.68E-08 mr1222 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
vg1223453821 NA 1.38E-13 mr1521 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
vg1223453821 NA 1.32E-06 mr1521 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
vg1223453821 9.36E-06 6.81E-07 mr1582 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
vg1223453821 3.49E-06 2.42E-06 mr1632 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
vg1223453821 6.16E-07 1.35E-07 mr1772 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
vg1223453821 NA 5.80E-06 mr1918 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
vg1223453821 NA 4.95E-06 mr1977 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
vg1223453821 NA 6.36E-06 mr1182_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