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

Detailed information for vg1217303672:

Variant ID: vg1217303672 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17303672
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATATTTTACTACTACAAAACGGTAAATATGGAACAATCTTATATAGGTGCCGGTTCTTGTTCACAACCGATGACACCTGTAAGGGGCCTCTCATCGGTG[C/T]
CGGTTGCGACTCGAGAATCAAAGGGTGGTTCCCAAGTCCCCACCGGCATCGAAATAGGGTTTCTGTGGTAGTGCTAGGGTTTGGATGACATGGATCGAAC

Reverse complement sequence

GTTCGATCCATGTCATCCAAACCCTAGCACTACCACAGAAACCCTATTTCGATGCCGGTGGGGACTTGGGAACCACCCTTTGATTCTCGAGTCGCAACCG[G/A]
CACCGATGAGAGGCCCCTTACAGGTGTCATCGGTTGTGAACAAGAACCGGCACCTATATAAGATTGTTCCATATTTACCGTTTTGTAGTAGTAAAATATA

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 55.90% 21.30% 0.36% 22.51% NA
All Indica  2759 37.40% 28.30% 0.51% 33.82% NA
All Japonica  1512 81.10% 12.90% 0.00% 6.02% NA
Aus  269 91.40% 1.10% 0.00% 7.43% NA
Indica I  595 9.60% 12.90% 0.34% 77.14% NA
Indica II  465 81.50% 4.50% 0.22% 13.76% NA
Indica III  913 27.20% 52.50% 0.44% 19.93% NA
Indica Intermediate  786 44.10% 26.00% 0.89% 29.01% NA
Temperate Japonica  767 96.60% 0.80% 0.00% 2.61% NA
Tropical Japonica  504 58.10% 31.30% 0.00% 10.52% NA
Japonica Intermediate  241 79.70% 12.90% 0.00% 7.47% NA
VI/Aromatic  96 86.50% 3.10% 1.04% 9.38% NA
Intermediate  90 60.00% 25.60% 2.22% 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
vg1217303672 C -> DEL N N silent_mutation Average:68.692; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N
vg1217303672 C -> T LOC_Os12g29220.1 intron_variant ; MODIFIER silent_mutation Average:68.692; most accessible tissue: Zhenshan97 root, score: 76.749 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217303672 NA 1.80E-06 mr1015 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
vg1217303672 NA 1.35E-06 mr1218 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
vg1217303672 NA 6.74E-07 mr1422 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
vg1217303672 NA 4.83E-08 mr1583 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
vg1217303672 6.82E-06 NA mr1083_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
vg1217303672 NA 1.82E-06 mr1092_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
vg1217303672 5.07E-06 NA mr1107_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
vg1217303672 NA 3.60E-06 mr1133_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
vg1217303672 NA 4.37E-07 mr1218_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
vg1217303672 5.08E-07 NA mr1226_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
vg1217303672 NA 9.38E-06 mr1460_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