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Detailed information for vg0703431101:

Variant ID: vg0703431101 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 3431101
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, C: 0.11, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GTGCTTCAGCCAAATTCAAGCTGGTAATGAAAATTATCAGACTGAGGTGTTAAGATTGGACCTCACCTCTAGATATCTTGGAAAGGTCATGAGAAAACTC[A/C]
TTAGCTGCAGCAAGGATCAAATCCTTAGGAGGCAATTCAGCTATGAAACATGCGCTTTGATTAACTGACAGCTGACTCACGCATGATTCAATCTGATTCT

Reverse complement sequence

AGAATCAGATTGAATCATGCGTGAGTCAGCTGTCAGTTAATCAAAGCGCATGTTTCATAGCTGAATTGCCTCCTAAGGATTTGATCCTTGCTGCAGCTAA[T/G]
GAGTTTTCTCATGACCTTTCCAAGATATCTAGAGGTGAGGTCCAATCTTAACACCTCAGTCTGATAATTTTCATTACCAGCTTGAATTTGGCTGAAGCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.00% 43.60% 0.13% 0.28% NA
All Indica  2759 35.80% 63.60% 0.14% 0.40% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 3.30% 96.70% 0.00% 0.00% NA
Indica I  595 84.70% 15.00% 0.00% 0.34% NA
Indica II  465 15.10% 84.10% 0.22% 0.65% NA
Indica III  913 15.90% 83.80% 0.11% 0.22% NA
Indica Intermediate  786 34.20% 65.00% 0.25% 0.51% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 60.00% 35.60% 2.22% 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
vg0703431101 A -> DEL LOC_Os07g06970.1 N frameshift_variant Average:52.151; most accessible tissue: Callus, score: 72.299 N N N N
vg0703431101 A -> C LOC_Os07g06970.1 missense_variant ; p.Asn638Lys; MODERATE nonsynonymous_codon Average:52.151; most accessible tissue: Callus, score: 72.299 benign -0.02 TOLERATED 0.58

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0703431101 NA 5.05E-07 mr1291 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
vg0703431101 NA 8.30E-06 mr1531 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
vg0703431101 NA 1.11E-17 mr1557 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
vg0703431101 NA 6.56E-06 mr1904 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
vg0703431101 NA 3.57E-16 mr1557_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
vg0703431101 NA 1.18E-07 mr1659_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
vg0703431101 NA 8.93E-06 mr1974_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