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Detailed information for vg1217945266:

Variant ID: vg1217945266 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17945266
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATATCACTATCATACAAACTTTTCCCCACGGCAACGCACATGATTTTATCTAGTTACTATGTGAGAGCATAATATATATTTTTCCACTATATATCTAT[C/A]
TATCTATCTATTATTATATACTAAAAGTCCATTAAACTTCCTACAAACGCTCCTAAGCCGCCACGTGACAATTCTATAAATGCTCCTAAGTCGCCATGTG

Reverse complement sequence

CACATGGCGACTTAGGAGCATTTATAGAATTGTCACGTGGCGGCTTAGGAGCGTTTGTAGGAAGTTTAATGGACTTTTAGTATATAATAATAGATAGATA[G/T]
ATAGATATATAGTGGAAAAATATATATTATGCTCTCACATAGTAACTAGATAAAATCATGTGCGTTGCCGTGGGGAAAAGTTTGTATGATAGTGATATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.70% 9.10% 10.92% 17.33% NA
All Indica  2759 63.80% 1.50% 12.11% 22.65% NA
All Japonica  1512 67.60% 21.60% 1.85% 8.93% NA
Aus  269 44.20% 5.90% 32.34% 17.47% NA
Indica I  595 55.50% 1.50% 18.32% 24.71% NA
Indica II  465 82.20% 0.20% 3.44% 14.19% NA
Indica III  913 62.20% 0.40% 14.02% 23.33% NA
Indica Intermediate  786 60.90% 3.40% 10.31% 25.32% NA
Temperate Japonica  767 84.50% 14.30% 0.26% 0.91% NA
Tropical Japonica  504 40.90% 35.50% 3.17% 20.44% NA
Japonica Intermediate  241 69.70% 15.80% 4.15% 10.37% NA
VI/Aromatic  96 8.30% 32.30% 56.25% 3.12% NA
Intermediate  90 61.10% 14.40% 14.44% 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
vg1217945266 C -> DEL N N silent_mutation Average:49.449; most accessible tissue: Minghui63 root, score: 67.149 N N N N
vg1217945266 C -> A LOC_Os12g30000-LOC_Os12g30020 intergenic_region ; MODIFIER silent_mutation Average:49.449; most accessible tissue: Minghui63 root, score: 67.149 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217945266 8.33E-07 NA mr1410 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
vg1217945266 1.00E-07 NA mr1410 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
vg1217945266 NA 1.12E-06 mr1068_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
vg1217945266 NA 1.23E-06 mr1072_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
vg1217945266 NA 6.76E-07 mr1110_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
vg1217945266 NA 5.56E-06 mr1112_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
vg1217945266 3.70E-07 NA mr1136_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
vg1217945266 NA 4.71E-06 mr1211_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
vg1217945266 5.61E-06 NA mr1410_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
vg1217945266 1.18E-06 NA mr1410_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