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Detailed information for vg1216110511:

Variant ID: vg1216110511 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16110511
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCATGCTACAGAGATTATAACAACAGTACAATGCTATTTCACATTGTTCACAACACAATAACATACTGTTTAACGATAACAACGAAATTCATTGAAATTA[T/C]
AACATATGAGTACTTGGTACGACAACATTAGGATACAATACTCAATAATTCGCAATACATGACTACTAATTTCATCACATTACATGACATAAATACTTAG

Reverse complement sequence

CTAAGTATTTATGTCATGTAATGTGATGAAATTAGTAGTCATGTATTGCGAATTATTGAGTATTGTATCCTAATGTTGTCGTACCAAGTACTCATATGTT[A/G]
TAATTTCAATGAATTTCGTTGTTATCGTTAAACAGTATGTTATTGTGTTGTGAACAATGTGAAATAGCATTGTACTGTTGTTATAATCTCTGTAGCATGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 28.30% 2.60% 21.43% 47.69% NA
All Indica  2759 9.00% 1.00% 35.70% 54.30% NA
All Japonica  1512 65.10% 0.50% 0.46% 33.93% NA
Aus  269 13.40% 10.80% 1.49% 74.35% NA
Indica I  595 17.00% 0.20% 4.03% 78.82% NA
Indica II  465 11.20% 0.90% 73.98% 13.98% NA
Indica III  913 1.40% 1.40% 40.53% 56.63% NA
Indica Intermediate  786 10.60% 1.10% 31.42% 56.87% NA
Temperate Japonica  767 95.60% 0.00% 0.00% 4.43% NA
Tropical Japonica  504 14.70% 0.60% 1.19% 83.53% NA
Japonica Intermediate  241 73.90% 1.70% 0.41% 24.07% NA
VI/Aromatic  96 28.10% 54.20% 0.00% 17.71% NA
Intermediate  90 43.30% 8.90% 18.89% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216110511 T -> C LOC_Os12g27390.1 intron_variant ; MODIFIER silent_mutation Average:24.087; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N
vg1216110511 T -> DEL N N silent_mutation Average:24.087; most accessible tissue: Minghui63 young leaf, score: 56.213 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216110511 NA 9.98E-06 mr1285 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
vg1216110511 NA 6.77E-09 mr1746 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
vg1216110511 NA 2.57E-06 mr1748 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
vg1216110511 NA 2.34E-07 mr1041_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
vg1216110511 NA 7.68E-06 mr1184_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
vg1216110511 1.30E-06 NA mr1186_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
vg1216110511 NA 4.41E-06 mr1278_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
vg1216110511 NA 9.20E-06 mr1284_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
vg1216110511 6.22E-06 1.03E-08 mr1293_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
vg1216110511 NA 1.85E-06 mr1294_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
vg1216110511 NA 2.78E-07 mr1329_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
vg1216110511 2.69E-08 3.75E-11 mr1369_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
vg1216110511 6.29E-08 4.13E-11 mr1453_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
vg1216110511 NA 6.63E-07 mr1497_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
vg1216110511 NA 3.65E-07 mr1508_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
vg1216110511 NA 3.87E-07 mr1524_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
vg1216110511 NA 1.76E-07 mr1604_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
vg1216110511 3.89E-07 2.05E-07 mr1616_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
vg1216110511 2.01E-07 1.57E-08 mr1652_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
vg1216110511 2.36E-06 NA 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
vg1216110511 NA 2.45E-08 mr1683_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
vg1216110511 NA 2.23E-08 mr1690_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
vg1216110511 NA 5.90E-07 mr1824_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
vg1216110511 NA 1.12E-09 mr1851_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