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Detailed information for vg0116413317:

Variant ID: vg0116413317 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16413317
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.54, A: 0.46, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


ACGCTGTTGTCGGTGAAACTGGATGTCATAGTAGTAGAACCTTGAGCACCAAGTCCCCCTACCTGGCACGCCACTGTCGACGGGGGATACCCGTAGACCG[A/G]
ATATAGAGGGTATTGGGGTACGCTGGTACGAGGATCTACGTAGTACGACATCAAGCAAACAGGAAACAGGGATTATACTGGTTCAGGCCCCTTGGCAGGT

Reverse complement sequence

ACCTGCCAAGGGGCCTGAACCAGTATAATCCCTGTTTCCTGTTTGCTTGATGTCGTACTACGTAGATCCTCGTACCAGCGTACCCCAATACCCTCTATAT[T/C]
CGGTCTACGGGTATCCCCCGTCGACAGTGGCGTGCCAGGTAGGGGGACTTGGTGCTCAAGGTTCTACTACTATGACATCCAGTTTCACCGACAACAGCGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 38.00% 6.30% 34.26% 21.50% NA
All Indica  2759 4.10% 9.10% 53.14% 33.60% NA
All Japonica  1512 95.90% 1.70% 2.05% 0.33% NA
Aus  269 33.10% 4.80% 34.94% 27.14% NA
Indica I  595 1.20% 4.70% 66.89% 27.23% NA
Indica II  465 4.90% 8.60% 41.29% 45.16% NA
Indica III  913 3.70% 12.80% 47.32% 36.14% NA
Indica Intermediate  786 6.40% 8.50% 56.49% 28.63% NA
Temperate Japonica  767 98.80% 0.40% 0.65% 0.13% NA
Tropical Japonica  504 94.40% 0.60% 4.56% 0.40% NA
Japonica Intermediate  241 89.60% 8.30% 1.24% 0.83% NA
VI/Aromatic  96 93.80% 0.00% 5.21% 1.04% NA
Intermediate  90 57.80% 5.60% 25.56% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0116413317 A -> G LOC_Os01g29270.1 missense_variant ; p.Ser18Pro; MODERATE nonsynonymous_codon ; S18L Average:57.057; most accessible tissue: Minghui63 flag leaf, score: 79.383 benign 1.307 DELETERIOUS 0.05
vg0116413317 A -> G LOC_Os01g29270.1 missense_variant ; p.Ser18Pro; MODERATE nonsynonymous_codon ; S18P Average:57.057; most accessible tissue: Minghui63 flag leaf, score: 79.383 benign -0.47 TOLERATED 1.00
vg0116413317 A -> DEL LOC_Os01g29270.1 N frameshift_variant Average:57.057; most accessible tissue: Minghui63 flag leaf, score: 79.383 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116413317 NA 3.62E-15 mr1164 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
vg0116413317 NA 9.43E-11 mr1172 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
vg0116413317 NA 6.41E-15 mr1228 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
vg0116413317 NA 3.07E-28 mr1298 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
vg0116413317 NA 7.16E-16 mr1323 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
vg0116413317 NA 1.89E-09 mr1352 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
vg0116413317 1.11E-06 NA mr1414 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
vg0116413317 NA 2.37E-23 mr1571 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
vg0116413317 NA 4.78E-20 mr1580 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
vg0116413317 NA 3.91E-11 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
vg0116413317 NA 4.58E-19 mr1627 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
vg0116413317 NA 3.62E-06 mr1646 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
vg0116413317 NA 3.05E-12 mr1744 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
vg0116413317 NA 1.75E-18 mr1825 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
vg0116413317 9.08E-06 NA mr1882 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
vg0116413317 NA 3.73E-22 mr1943 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
vg0116413317 NA 1.72E-48 mr1519_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
vg0116413317 NA 4.93E-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
vg0116413317 NA 5.67E-25 mr1916_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