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Detailed information for vg1204723475:

Variant ID: vg1204723475 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 4723475
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCATGAAAGCGAAGACTCCATGGATAGCGGCGAAGGCTAGCCGGGGTGAAGACATAGAGGCCCATCAACGGTGGTGTGACCAACCAATCGTGAATGCGA[T/G]
GACACCAGTCGGCGGTGACGGAGGCAAGCCGACGTTGAAGATGTATGTGCCCATCGATGGCGGTGTGACCAACCAGCCGTGTAGGCGAAGGTACTAGTAG

Reverse complement sequence

CTACTAGTACCTTCGCCTACACGGCTGGTTGGTCACACCGCCATCGATGGGCACATACATCTTCAACGTCGGCTTGCCTCCGTCACCGCCGACTGGTGTC[A/C]
TCGCATTCACGATTGGTTGGTCACACCACCGTTGATGGGCCTCTATGTCTTCACCCCGGCTAGCCTTCGCCGCTATCCATGGAGTCTTCGCTTTCATGGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.10% 33.50% 0.13% 0.21% NA
All Indica  2759 97.30% 2.40% 0.07% 0.29% NA
All Japonica  1512 12.40% 87.40% 0.20% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.00% 0.17% NA
Indica II  465 96.80% 3.00% 0.00% 0.22% NA
Indica III  913 98.40% 1.20% 0.11% 0.33% NA
Indica Intermediate  786 95.20% 4.30% 0.13% 0.38% NA
Temperate Japonica  767 4.80% 95.20% 0.00% 0.00% NA
Tropical Japonica  504 8.70% 91.10% 0.20% 0.00% NA
Japonica Intermediate  241 44.40% 54.80% 0.83% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 37.80% 58.90% 1.11% 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
vg1204723475 T -> DEL N N silent_mutation Average:65.259; most accessible tissue: Zhenshan97 young leaf, score: 87.153 N N N N
vg1204723475 T -> G LOC_Os12g09030.1 upstream_gene_variant ; 1664.0bp to feature; MODIFIER silent_mutation Average:65.259; most accessible tissue: Zhenshan97 young leaf, score: 87.153 N N N N
vg1204723475 T -> G LOC_Os12g09030-LOC_Os12g09050 intergenic_region ; MODIFIER silent_mutation Average:65.259; most accessible tissue: Zhenshan97 young leaf, score: 87.153 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1204723475 NA 2.47E-06 mr1117 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
vg1204723475 1.39E-06 1.48E-08 mr1120 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
vg1204723475 NA 7.49E-06 mr1123 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
vg1204723475 NA 3.72E-06 mr1242 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
vg1204723475 NA 8.72E-06 mr1247 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
vg1204723475 2.16E-06 NA mr1691 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
vg1204723475 8.03E-08 7.69E-10 mr1691 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
vg1204723475 5.35E-07 NA mr1693 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
vg1204723475 1.17E-08 1.05E-13 mr1693 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
vg1204723475 1.50E-06 5.66E-08 mr1720 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
vg1204723475 NA 8.45E-07 mr1117_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
vg1204723475 NA 7.47E-06 mr1119_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
vg1204723475 NA 7.90E-07 mr1496_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
vg1204723475 1.38E-06 NA mr1679_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
vg1204723475 4.46E-06 2.14E-09 mr1691_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
vg1204723475 NA 3.77E-08 mr1720_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