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Detailed information for vg0314127667:

Variant ID: vg0314127667 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14127667
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.58, C: 0.42, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTTCTCGTGCTGGGGGCTATATATACTCGGGCCATTCCCACAAGGACAGGGCGGCTACAAGTTCCTATTCGTGGCGATCGACAAATTCACTAAATGGA[C/T]
CGAAGCGGTACCCACGGGGGAAATCAAGGCCGCCAACGCCATCAAGTTCATCAAGGGGATATTTTGCAGATACGGACTACCGCATCGCATCATTACAGAC

Reverse complement sequence

GTCTGTAATGATGCGATGCGGTAGTCCGTATCTGCAAAATATCCCCTTGATGAACTTGATGGCGTTGGCGGCCTTGATTTCCCCCGTGGGTACCGCTTCG[G/A]
TCCATTTAGTGAATTTGTCGATCGCCACGAATAGGAACTTGTAGCCGCCCTGTCCTTGTGGGAATGGCCCGAGTATATATAGCCCCCAGCACGAGAACGG

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 41.80% 34.70% 9.48% 14.07% NA
All Indica  2759 59.90% 3.80% 15.73% 20.55% NA
All Japonica  1512 0.80% 93.50% 0.13% 5.62% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 28.90% 7.20% 19.33% 44.54% NA
Indica II  465 46.90% 4.30% 20.86% 27.96% NA
Indica III  913 90.40% 0.40% 5.48% 3.72% NA
Indica Intermediate  786 55.70% 4.80% 21.88% 17.56% NA
Temperate Japonica  767 0.10% 91.40% 0.00% 8.47% NA
Tropical Japonica  504 1.40% 95.20% 0.40% 2.98% NA
Japonica Intermediate  241 1.70% 96.30% 0.00% 2.07% NA
VI/Aromatic  96 22.90% 74.00% 2.08% 1.04% NA
Intermediate  90 31.10% 44.40% 11.11% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314127667 C -> T LOC_Os03g24790.1 missense_variant ; p.Thr311Ile; MODERATE nonsynonymous_codon ; T311I Average:12.874; most accessible tissue: Minghui63 young leaf, score: 21.268 benign -0.54 TOLERATED 1.00
vg0314127667 C -> DEL LOC_Os03g24790.1 N frameshift_variant Average:12.874; most accessible tissue: Minghui63 young leaf, score: 21.268 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314127667 NA 3.63E-06 mr1066 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
vg0314127667 NA 2.00E-18 mr1133 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
vg0314127667 NA 6.08E-13 mr1322 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
vg0314127667 NA 8.46E-11 mr1325 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
vg0314127667 NA 5.37E-06 mr1425 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
vg0314127667 NA 7.48E-09 mr1527 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
vg0314127667 NA 2.18E-08 mr1532 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
vg0314127667 NA 9.52E-12 mr1553 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
vg0314127667 NA 6.36E-07 mr1574 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
vg0314127667 NA 4.56E-12 mr1623 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
vg0314127667 NA 5.41E-11 mr1714 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
vg0314127667 NA 1.24E-06 mr1781 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
vg0314127667 NA 9.86E-21 mr1817 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
vg0314127667 NA 1.96E-14 mr1133_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
vg0314127667 NA 2.60E-07 mr1821_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