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Detailed information for vg1214381489:

Variant ID: vg1214381489 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 14381489
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, C: 0.47, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTAAAAGCGGTACCGGACAAAGATAAAGAAAACAAGCGCAATTTAAAAGTATCACTATTAGCCTCACCACATTGTGCTAAAAATTGACCTACATGCTC[A/C]
CATGTGGTTCTACAATCTTCACCACTAAACTTGGTAAATTCGGGAACTCTATAATTACAAGCAAACAGCACATTATCATAATAGTCAGGATACGACTTTT

Reverse complement sequence

AAAAGTCGTATCCTGACTATTATGATAATGTGCTGTTTGCTTGTAATTATAGAGTTCCCGAATTTACCAAGTTTAGTGGTGAAGATTGTAGAACCACATG[T/G]
GAGCATGTAGGTCAATTTTTAGCACAATGTGGTGAGGCTAATAGTGATACTTTTAAATTGCGCTTGTTTTCTTTATCTTTGTCCGGTACCGCTTTTACAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 22.50% 13.00% 0.47% 63.99% NA
All Indica  2759 10.00% 20.50% 0.62% 68.87% NA
All Japonica  1512 49.70% 2.80% 0.07% 47.42% NA
Aus  269 3.00% 0.40% 0.00% 96.65% NA
Indica I  595 21.80% 1.80% 0.34% 75.97% NA
Indica II  465 11.80% 35.50% 1.51% 51.18% NA
Indica III  913 2.30% 24.20% 0.33% 73.17% NA
Indica Intermediate  786 8.90% 21.50% 0.64% 68.96% NA
Temperate Japonica  767 79.00% 5.10% 0.13% 15.78% NA
Tropical Japonica  504 12.50% 0.00% 0.00% 87.50% NA
Japonica Intermediate  241 34.00% 1.70% 0.00% 64.32% NA
VI/Aromatic  96 3.10% 1.00% 1.04% 94.79% NA
Intermediate  90 28.90% 5.60% 3.33% 62.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1214381489 A -> C LOC_Os12g25050.1 missense_variant ; p.Val212Gly; MODERATE nonsynonymous_codon ; V212G Average:8.85; most accessible tissue: Callus, score: 36.735 unknown unknown TOLERATED 0.43
vg1214381489 A -> DEL LOC_Os12g25050.1 N frameshift_variant Average:8.85; most accessible tissue: Callus, score: 36.735 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1214381489 NA 4.01E-06 mr1013 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
vg1214381489 NA 5.08E-10 mr1018 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
vg1214381489 9.33E-07 NA mr1019 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
vg1214381489 NA 4.98E-10 mr1019 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
vg1214381489 NA 6.59E-15 mr1023 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
vg1214381489 NA 9.54E-07 mr1031 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
vg1214381489 NA 2.91E-06 mr1056 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
vg1214381489 NA 1.38E-14 mr1079 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
vg1214381489 NA 1.20E-15 mr1142 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
vg1214381489 NA 4.67E-09 mr1364 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
vg1214381489 NA 9.77E-07 mr1382 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
vg1214381489 NA 1.45E-08 mr1443 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
vg1214381489 NA 2.20E-16 mr1489 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
vg1214381489 NA 2.62E-15 mr1491 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
vg1214381489 NA 1.77E-06 mr1543 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
vg1214381489 NA 1.82E-14 mr1778 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
vg1214381489 NA 2.30E-09 mr1022_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
vg1214381489 2.65E-06 1.28E-19 mr1023_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
vg1214381489 NA 1.74E-15 mr1079_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
vg1214381489 NA 3.57E-06 mr1346_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
vg1214381489 NA 2.14E-17 mr1489_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
vg1214381489 NA 3.88E-08 mr1554_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
vg1214381489 NA 7.03E-06 mr1577_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
vg1214381489 NA 3.30E-06 mr1730_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
vg1214381489 NA 6.46E-15 mr1778_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
vg1214381489 NA 2.19E-07 mr1792_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