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Detailed information for vg1223833401:

Variant ID: vg1223833401 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23833401
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTGATCATGTTGTTGATTCTATGTAGAACCCAGTGAAACCTCTGGGGAAAGAGCCCACTGAACCGATTGATGTTGTGCTACATAGCGAGATTCGCTC[T/G]
GTCGGTCGCGCCAGGTTCGATCACCAAGTGAGTAGTAAATTTTGTAATGCTAGATCGCCCTCGACGAGTTCCTAAACGTCTTGACGGTTTATCTTCAATC

Reverse complement sequence

GATTGAAGATAAACCGTCAAGACGTTTAGGAACTCGTCGAGGGCGATCTAGCATTACAAAATTTACTACTCACTTGGTGATCGAACCTGGCGCGACCGAC[A/C]
GAGCGAATCTCGCTATGTAGCACAACATCAATCGGTTCAGTGGGCTCTTTCCCCAGAGGTTTCACTGGGTTCTACATAGAATCAACAACATGATCAACAC

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 72.00% 28.00% 0.00% 0.00% NA
All Indica  2759 98.20% 1.80% 0.00% 0.00% NA
All Japonica  1512 24.30% 75.70% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 16.00% 84.00% 0.00% 0.00% NA
Tropical Japonica  504 28.20% 71.80% 0.00% 0.00% NA
Japonica Intermediate  241 42.70% 57.30% 0.00% 0.00% NA
VI/Aromatic  96 12.50% 87.50% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 0.00% 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
vg1223833401 T -> G LOC_Os12g38790.1 synonymous_variant ; p.Ser332Ser; LOW synonymous_codon Average:61.536; most accessible tissue: Zhenshan97 flower, score: 71.992 N N N N
vg1223833401 T -> G LOC_Os12g38790.1 synonymous_variant ; p.Ser332Ser; LOW nonsynonymous_codon ; S332A Average:61.536; most accessible tissue: Zhenshan97 flower, score: 71.992 unknown unknown TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223833401 NA 1.14E-15 mr1118 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
vg1223833401 NA 2.70E-18 mr1242 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
vg1223833401 NA 6.38E-06 mr1681 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
vg1223833401 NA 1.24E-06 mr1159_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
vg1223833401 NA 5.52E-08 mr1299_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
vg1223833401 NA 2.40E-07 mr1321_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
vg1223833401 8.66E-06 NA mr1428_2 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
vg1223833401 NA 2.21E-09 mr1645_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
vg1223833401 NA 1.44E-07 mr1648_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
vg1223833401 NA 4.33E-06 mr1655_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
vg1223833401 6.41E-07 1.34E-23 mr1657_2 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
vg1223833401 NA 1.94E-13 mr1722_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
vg1223833401 NA 1.35E-06 mr1727_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