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Detailed information for vg0901968940:

Variant ID: vg0901968940 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1968940
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, C: 0.01, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TCCTATAGTCCAGAAAAGGCCAACAAAAAAAAATAGTAGATTAGTTTTCCCGTGATCCTATAGACCATTGTGCTTTTTTTTACTAGTACTGCTTAGTTAA[G/C]
GCTTGTTGAGTTTTCGATTGCATCGGTTGTGTTAATTTGCTGGTCTTAGTGTTAGGCGATTAGAGTTTCGAGTTCTTGCCACCACCGCACATCGCCACCT

Reverse complement sequence

AGGTGGCGATGTGCGGTGGTGGCAAGAACTCGAAACTCTAATCGCCTAACACTAAGACCAGCAAATTAACACAACCGATGCAATCGAAAACTCAACAAGC[C/G]
TTAACTAAGCAGTACTAGTAAAAAAAAGCACAATGGTCTATAGGATCACGGGAAAACTAATCTACTATTTTTTTTTGTTGGCCTTTTCTGGACTATAGGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.90% 13.00% 0.02% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 65.30% 34.70% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 22.80% 77.20% 0.00% 0.00% NA
Japonica Intermediate  241 51.00% 48.50% 0.41% 0.00% NA
VI/Aromatic  96 53.10% 46.90% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0901968940 G -> C LOC_Os09g03870.1 intron_variant ; MODIFIER silent_mutation Average:34.372; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901968940 2.74E-06 1.56E-08 mr1639 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
vg0901968940 NA 3.12E-06 mr1211_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
vg0901968940 NA 1.21E-06 mr1554_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
vg0901968940 NA 8.73E-08 mr1578_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
vg0901968940 NA 1.12E-13 mr1864_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