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Detailed information for vg0704068888:

Variant ID: vg0704068888 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4068888
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTCAGATACAAAGCTACACAGAGAAAAGGACAAGGACAAAAACAGATACTCCCGAATTACTACGGCTAATCTGCATAATAAGAAGGCAACACCAGCCA[C/T]
GAGTACCAAGAGTACAACGGTGCAATTTTTACACGGTTGACTAAGAGTTTAGTAGTGATTCTAGTGAAGTTCATGGCACTAACAGCGAGTAGTCACTGAG

Reverse complement sequence

CTCAGTGACTACTCGCTGTTAGTGCCATGAACTTCACTAGAATCACTACTAAACTCTTAGTCAACCGTGTAAAAATTGCACCGTTGTACTCTTGGTACTC[G/A]
TGGCTGGTGTTGCCTTCTTATTATGCAGATTAGCCGTAGTAATTCGGGAGTATCTGTTTTTGTCCTTGTCCTTTTCTCTGTGTAGCTTTGTATCTGAAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 6.90% 0.40% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 83.90% 14.80% 1.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 97.90% 2.00% 0.13% 0.00% NA
Tropical Japonica  504 66.70% 30.80% 2.58% 0.00% NA
Japonica Intermediate  241 75.50% 22.40% 2.07% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0704068888 C -> T LOC_Os07g08040.1 downstream_gene_variant ; 1926.0bp to feature; MODIFIER silent_mutation Average:60.117; most accessible tissue: Minghui63 flag leaf, score: 72.028 N N N N
vg0704068888 C -> T LOC_Os07g08030.1 intron_variant ; MODIFIER silent_mutation Average:60.117; most accessible tissue: Minghui63 flag leaf, score: 72.028 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704068888 NA 5.91E-10 mr1057 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
vg0704068888 NA 1.10E-06 mr1368 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
vg0704068888 7.96E-06 NA mr1871 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
vg0704068888 4.09E-06 4.09E-06 mr1891 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
vg0704068888 NA 2.43E-11 mr1057_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
vg0704068888 NA 9.88E-06 mr1851_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