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Detailed information for vg1000624564:

Variant ID: vg1000624564 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 624564
Reference Allele: GAlternative Allele: C,A
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTAAGTTCAACAATAGTTTAATTATCTCGTTCGTACACGTTTCGCTCGCGTTCGTTCGCGTTCGTTCACGTTCGTTCGCGTTTCGTTCACGTTCGTTC[G/C,A]
TGTTCGTTCACGTTTCGTTCATGTTCGTTCACGTTTCGTTCGCGTTTCAATCACGTTCGTTTACGTCGTTCGCATTCGTTCACGTTTCGTTCGCGTTCGT

Reverse complement sequence

ACGAACGCGAACGAAACGTGAACGAATGCGAACGACGTAAACGAACGTGATTGAAACGCGAACGAAACGTGAACGAACATGAACGAAACGTGAACGAACA[C/G,T]
GAACGAACGTGAACGAAACGCGAACGAACGTGAACGAACGCGAACGAACGCGAGCGAAACGTGTACGAACGAGATAATTAAACTATTGTTGAACTTAGCA

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 61.70% 12.80% 6.03% 19.47% A: 0.04%
All Indica  2759 72.90% 1.90% 7.97% 17.14% A: 0.04%
All Japonica  1512 44.10% 24.30% 3.64% 27.91% NA
Aus  269 49.80% 47.20% 0.74% 2.23% NA
Indica I  595 55.50% 0.20% 6.05% 38.32% NA
Indica II  465 94.20% 0.90% 1.29% 3.66% NA
Indica III  913 71.30% 3.50% 14.79% 10.41% NA
Indica Intermediate  786 75.40% 2.00% 5.47% 16.92% A: 0.13%
Temperate Japonica  767 13.00% 33.60% 6.13% 47.20% NA
Tropical Japonica  504 89.30% 6.20% 1.19% 3.37% NA
Japonica Intermediate  241 48.50% 32.80% 0.83% 17.84% NA
VI/Aromatic  96 47.90% 37.50% 3.12% 10.42% A: 1.04%
Intermediate  90 61.10% 23.30% 5.56% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1000624564 G -> C LOC_Os10g01984.1 intron_variant ; MODIFIER silent_mutation Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg1000624564 G -> A LOC_Os10g01984.1 intron_variant ; MODIFIER silent_mutation Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N
vg1000624564 G -> DEL N N silent_mutation Average:21.366; most accessible tissue: Minghui63 panicle, score: 42.799 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1000624564 2.49E-06 NA mr1002 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
vg1000624564 6.98E-17 4.53E-33 mr1300 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
vg1000624564 4.97E-10 2.17E-14 mr1300 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
vg1000624564 1.37E-18 4.15E-45 mr1310 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
vg1000624564 4.49E-11 1.13E-17 mr1310 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
vg1000624564 NA 2.83E-09 mr1457 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
vg1000624564 NA 2.18E-06 mr1548 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
vg1000624564 NA 4.10E-06 mr1912 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
vg1000624564 7.87E-24 8.59E-59 mr1926 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
vg1000624564 9.93E-12 5.17E-20 mr1926 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
vg1000624564 8.26E-10 9.90E-14 mr1959 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
vg1000624564 9.47E-09 6.50E-11 mr1959 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
vg1000624564 7.57E-28 3.74E-50 mr1310_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
vg1000624564 4.45E-17 1.13E-27 mr1310_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
vg1000624564 2.08E-13 1.64E-22 mr1959_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
vg1000624564 9.70E-10 2.79E-16 mr1959_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