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Detailed information for vg0314815996:

Variant ID: vg0314815996 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14815996
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


TATAATTCATAATTTGTTGTAGATCTATGTGTTTGTGTGTTCTAAGTTAGTTCTTCACAGGTGGCCCATTGGTCCATCCCTTGGCCAATGTTTACACAGG[C/T]
GGGTTCTACTTTCAACTCGCCTGTGTCATAAATGGGGTATAGGAAAAACACATTATTGTATGATTGGATTTTTTTTTCGATTAATTTGGATGTGTTGTTT

Reverse complement sequence

AAACAACACATCCAAATTAATCGAAAAAAAAATCCAATCATACAATAATGTGTTTTTCCTATACCCCATTTATGACACAGGCGAGTTGAAAGTAGAACCC[G/A]
CCTGTGTAAACATTGGCCAAGGGATGGACCAATGGGCCACCTGTGAAGAACTAACTTAGAACACACAAACACATAGATCTACAACAAATTATGAATTATA

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 71.90% 7.00% 0.02% 21.10% NA
All Indica  2759 74.70% 0.00% 0.00% 25.30% NA
All Japonica  1512 79.40% 19.60% 0.00% 0.93% NA
Aus  269 3.70% 0.40% 0.37% 95.54% NA
Indica I  595 52.10% 0.00% 0.00% 47.90% NA
Indica II  465 61.30% 0.00% 0.00% 38.71% NA
Indica III  913 90.70% 0.00% 0.00% 9.31% NA
Indica Intermediate  786 81.20% 0.00% 0.00% 18.83% NA
Temperate Japonica  767 96.70% 3.10% 0.00% 0.13% NA
Tropical Japonica  504 55.00% 43.10% 0.00% 1.98% NA
Japonica Intermediate  241 75.50% 23.20% 0.00% 1.24% NA
VI/Aromatic  96 70.80% 24.00% 0.00% 5.21% NA
Intermediate  90 65.60% 8.90% 0.00% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0314815996 C -> T LOC_Os03g25890-LOC_Os03g25900 intergenic_region ; MODIFIER silent_mutation Average:60.124; most accessible tissue: Callus, score: 82.786 N N N N
vg0314815996 C -> DEL N N silent_mutation Average:60.124; most accessible tissue: Callus, score: 82.786 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314815996 1.32E-09 NA Grain_length All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314815996 1.65E-06 5.50E-18 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314815996 NA 8.66E-06 mr1125 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
vg0314815996 NA 6.93E-06 mr1192 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
vg0314815996 NA 2.33E-07 mr1206 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
vg0314815996 NA 3.74E-07 mr1338 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
vg0314815996 NA 5.37E-06 mr1502 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
vg0314815996 NA 5.81E-06 mr1502 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
vg0314815996 NA 2.63E-10 mr1539 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
vg0314815996 NA 4.38E-06 mr1620 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
vg0314815996 NA 3.35E-09 mr1398_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
vg0314815996 NA 3.27E-08 mr1422_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
vg0314815996 NA 1.46E-12 mr1533_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
vg0314815996 NA 4.70E-06 mr1583_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
vg0314815996 NA 1.54E-07 mr1606_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
vg0314815996 NA 3.32E-07 mr1727_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
vg0314815996 NA 2.19E-08 mr1819_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
vg0314815996 NA 7.46E-06 mr1830_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
vg0314815996 NA 5.25E-07 mr1873_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
vg0314815996 NA 6.33E-12 mr1905_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
vg0314815996 NA 8.49E-08 mr1905_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
vg0314815996 NA 4.15E-10 mr1916_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
vg0314815996 NA 3.51E-09 mr1942_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