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Detailed information for vg0319434107:

Variant ID: vg0319434107 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 19434107
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CATTGGCATCCTTGTTAGGCTTGCCACAGAATGGGCTAGCCTTCGCCATCATGATGAGGCTGGACTTCAAGTCGAAATCCACGTCTCCCATGTTGATTTG[T/C]
GGCCCAATGGCCACATTGTCAGCAGAGGGAGCAGCAAACTCGCGAAGGGTCTTGTCAGCCATAGTCTTGAAGGTTGGTGGCGCTGGTACGACTGGTTTCT

Reverse complement sequence

AGAAACCAGTCGTACCAGCGCCACCAACCTTCAAGACTATGGCTGACAAGACCCTTCGCGAGTTTGCTGCTCCCTCTGCTGACAATGTGGCCATTGGGCC[A/G]
CAAATCAACATGGGAGACGTGGATTTCGACTTGAAGTCCAGCCTCATCATGATGGCGAAGGCTAGCCCATTCTGTGGCAAGCCTAACAAGGATGCCAATG

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 64.30% 31.40% 1.21% 3.07% NA
All Indica  2759 91.80% 2.10% 1.85% 4.24% NA
All Japonica  1512 12.80% 85.50% 0.00% 1.65% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 89.20% 1.20% 6.22% 3.36% NA
Indica II  465 94.20% 2.60% 0.65% 2.58% NA
Indica III  913 93.30% 1.00% 0.33% 5.37% NA
Indica Intermediate  786 90.60% 3.80% 1.02% 4.58% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 34.30% 65.50% 0.00% 0.20% NA
Japonica Intermediate  241 7.50% 82.60% 0.00% 9.96% NA
VI/Aromatic  96 25.00% 72.90% 0.00% 2.08% NA
Intermediate  90 50.00% 42.20% 6.67% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0319434107 T -> C LOC_Os03g34102.1 synonymous_variant ; p.Pro21Pro; LOW synonymous_codon Average:59.223; most accessible tissue: Minghui63 flag leaf, score: 79.962 N N N N
vg0319434107 T -> C LOC_Os03g34102.1 synonymous_variant ; p.Pro21Pro; LOW nonsynonymous_codon ; P21L Average:59.223; most accessible tissue: Minghui63 flag leaf, score: 79.962 benign 0.336 TOLERATED 0.10
vg0319434107 T -> DEL LOC_Os03g34102.1 N frameshift_variant Average:59.223; most accessible tissue: Minghui63 flag leaf, score: 79.962 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0319434107 NA 3.38E-07 mr1136 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
vg0319434107 NA 1.48E-07 mr1217 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
vg0319434107 NA 4.01E-06 mr1334 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
vg0319434107 5.23E-06 NA mr1718 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
vg0319434107 1.52E-14 2.74E-19 mr1718 Ind_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
vg0319434107 3.12E-06 NA mr1750 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
vg0319434107 3.46E-09 1.69E-20 mr1750 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
vg0319434107 NA 3.82E-07 mr1785 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
vg0319434107 NA 2.41E-06 mr1830 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
vg0319434107 NA 4.09E-07 mr1845 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
vg0319434107 NA 9.96E-16 mr1933 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
vg0319434107 NA 1.76E-08 mr1136_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
vg0319434107 5.57E-06 NA mr1718_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
vg0319434107 2.53E-11 1.29E-18 mr1718_2 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
vg0319434107 NA 4.51E-11 mr1722_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
vg0319434107 7.09E-09 1.43E-27 mr1750_2 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
vg0319434107 NA 2.72E-06 mr1785_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
vg0319434107 NA 5.64E-14 mr1827_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
vg0319434107 NA 4.38E-22 mr1933_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