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Detailed information for vg0710335701:

Variant ID: vg0710335701 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 10335701
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCCCTTGCGGAGGCGAAATCGAAGCCTTCACAACTTTCCATGGCACACCACAACCTTGGGTGCTCACCGGCAACGCCTAGTCGTCTAGGAGACCTTAGT[A/C]
CCCAGGAGTAACAATCACAATCGAAGCTTTGCTTGCTATGAACTCGAGTACTCAAAGTATGTAGTGAAGCTCACTAGCTCTCAACTTCTCAATCCAACTC

Reverse complement sequence

GAGTTGGATTGAGAAGTTGAGAGCTAGTGAGCTTCACTACATACTTTGAGTACTCGAGTTCATAGCAAGCAAAGCTTCGATTGTGATTGTTACTCCTGGG[T/G]
ACTAAGGTCTCCTAGACGACTAGGCGTTGCCGGTGAGCACCCAAGGTTGTGGTGTGCCATGGAAAGTTGTGAAGGCTTCGATTTCGCCTCCGCAAGGGAA

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 30.00% 11.50% 0.42% 58.13% NA
All Indica  2759 5.30% 2.80% 0.65% 91.26% NA
All Japonica  1512 72.20% 23.50% 0.00% 4.37% NA
Aus  269 50.90% 9.30% 0.00% 39.78% NA
Indica I  595 9.10% 0.30% 0.34% 90.25% NA
Indica II  465 6.70% 0.00% 1.08% 92.26% NA
Indica III  913 1.40% 1.60% 0.66% 96.28% NA
Indica Intermediate  786 6.00% 7.80% 0.64% 85.62% NA
Temperate Japonica  767 57.50% 40.80% 0.00% 1.69% NA
Tropical Japonica  504 89.70% 0.60% 0.00% 9.72% NA
Japonica Intermediate  241 82.20% 16.20% 0.00% 1.66% NA
VI/Aromatic  96 4.20% 81.20% 0.00% 14.58% NA
Intermediate  90 43.30% 7.80% 2.22% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0710335701 A -> DEL N N silent_mutation Average:11.58; most accessible tissue: Callus, score: 55.093 N N N N
vg0710335701 A -> C LOC_Os07g17490-LOC_Os07g17500 intergenic_region ; MODIFIER silent_mutation Average:11.58; most accessible tissue: Callus, score: 55.093 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0710335701 NA 1.12E-14 mr1035 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
vg0710335701 NA 6.92E-06 mr1387 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
vg0710335701 NA 2.41E-18 mr1552 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
vg0710335701 NA 3.08E-13 mr1626 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
vg0710335701 NA 7.60E-12 mr1666 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
vg0710335701 NA 9.48E-07 mr1761 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
vg0710335701 NA 2.15E-12 mr1666_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
vg0710335701 NA 4.40E-11 mr1761_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