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Detailed information for vg0619155361:

Variant ID: vg0619155361 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19155361
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, C: 0.08, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ACAGTGCAGCCCATCTACCTTCTCATGCCCTCAAGGAGACCAAAGAAGCCCTAGGTCTCCTTGACACAAAAGATAAGGAAGTTCCTATGGGCGGGGACAA[G/C]
GGCCATCACAGGGGGGAAATGCATGATTAACTGGAAAAAGACGTGCATCCCAACCACACCAGGAGGACTGGGAGTTCTCAATATGCAGAAGTTCATGAGG

Reverse complement sequence

CCTCATGAACTTCTGCATATTGAGAACTCCCAGTCCTCCTGGTGTGGTTGGGATGCACGTCTTTTTCCAGTTAATCATGCATTTCCCCCCTGTGATGGCC[C/G]
TTGTCCCCGCCCATAGGAACTTCCTTATCTTTTGTGTCAAGGAGACCTAGGGCTTCTTTGGTCTCCTTGAGGGCATGAGAAGGTAGATGGGCTGCACTGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.20% 42.10% 0.21% 1.50% NA
All Indica  2759 88.50% 11.00% 0.11% 0.40% NA
All Japonica  1512 3.60% 92.60% 0.26% 3.57% NA
Aus  269 42.80% 57.20% 0.00% 0.00% NA
Indica I  595 92.90% 5.90% 0.17% 1.01% NA
Indica II  465 94.60% 5.20% 0.00% 0.22% NA
Indica III  913 91.30% 8.30% 0.11% 0.22% NA
Indica Intermediate  786 78.10% 21.50% 0.13% 0.25% NA
Temperate Japonica  767 4.60% 91.30% 0.26% 3.91% NA
Tropical Japonica  504 1.80% 96.80% 0.00% 1.39% NA
Japonica Intermediate  241 4.10% 88.00% 0.83% 7.05% NA
VI/Aromatic  96 5.20% 90.60% 0.00% 4.17% NA
Intermediate  90 43.30% 51.10% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619155361 G -> C LOC_Os06g32900.1 missense_variant ; p.Lys927Asn; MODERATE nonsynonymous_codon ; K927N Average:56.462; most accessible tissue: Zhenshan97 young leaf, score: 82.763 unknown unknown DELETERIOUS 0.00
vg0619155361 G -> DEL LOC_Os06g32900.1 N frameshift_variant Average:56.462; most accessible tissue: Zhenshan97 young leaf, score: 82.763 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619155361 NA 6.02E-07 mr1042_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
vg0619155361 NA 5.05E-08 mr1043_2 Jap_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
vg0619155361 NA 1.68E-07 mr1111_2 Ind_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
vg0619155361 NA 3.13E-07 mr1167_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
vg0619155361 NA 5.55E-07 mr1185_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
vg0619155361 2.50E-06 2.70E-09 mr1269_2 Jap_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
vg0619155361 NA 3.14E-07 mr1291_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
vg0619155361 NA 8.38E-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
vg0619155361 NA 9.99E-06 mr1456_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
vg0619155361 8.33E-06 2.00E-08 mr1479_2 Jap_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
vg0619155361 NA 1.25E-07 mr1502_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
vg0619155361 NA 8.92E-06 mr1638_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
vg0619155361 6.21E-06 7.52E-08 mr1677_2 Jap_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
vg0619155361 NA 7.98E-12 mr1680_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
vg0619155361 NA 7.30E-08 mr1680_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
vg0619155361 NA 2.65E-07 mr1726_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
vg0619155361 NA 3.05E-06 mr1736_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
vg0619155361 NA 1.75E-06 mr1740_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