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Detailed information for vg0614036364:

Variant ID: vg0614036364 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14036364
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTATTATGCCGCCGTCGTTGGGCGTCTACGTCTTCACCGACCGGCTTGCCTTTGCCGCCGCCGACTAGTGTCTTCGCCTGCATGACTGGTCTATTATGC[C/T]
GTCGTTGTTGGGCGTCAACGCTTTCACCGACTGGCTTGCCTTCGCCACTGCCGACTGGTGTCTCCGCCTGCACGGCTGGCCTATTATGCCACCGTTGTTG

Reverse complement sequence

CAACAACGGTGGCATAATAGGCCAGCCGTGCAGGCGGAGACACCAGTCGGCAGTGGCGAAGGCAAGCCAGTCGGTGAAAGCGTTGACGCCCAACAACGAC[G/A]
GCATAATAGACCAGTCATGCAGGCGAAGACACTAGTCGGCGGCGGCAAAGGCAAGCCGGTCGGTGAAGACGTAGACGCCCAACGACGGCGGCATAATAGA

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 47.80% 4.50% 4.72% 42.95% NA
All Indica  2759 27.20% 0.60% 5.76% 66.44% NA
All Japonica  1512 78.30% 12.80% 3.04% 5.89% NA
Aus  269 65.40% 0.00% 3.35% 31.23% NA
Indica I  595 35.00% 0.00% 2.52% 62.52% NA
Indica II  465 45.60% 0.90% 4.09% 49.46% NA
Indica III  913 9.70% 0.10% 8.32% 81.82% NA
Indica Intermediate  786 30.80% 1.40% 6.23% 61.58% NA
Temperate Japonica  767 96.00% 1.20% 0.91% 1.96% NA
Tropical Japonica  504 46.00% 34.70% 7.34% 11.90% NA
Japonica Intermediate  241 89.60% 3.70% 0.83% 5.81% NA
VI/Aromatic  96 90.60% 0.00% 2.08% 7.29% NA
Intermediate  90 66.70% 6.70% 7.78% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614036364 C -> T LOC_Os06g24030.1 missense_variant ; p.Pro2Leu; MODERATE nonsynonymous_codon ; P2L Average:31.6; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 unknown unknown DELETERIOUS 0.03
vg0614036364 C -> DEL LOC_Os06g24030.1 N frameshift_variant Average:31.6; most accessible tissue: Zhenshan97 flag leaf, score: 73.119 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0614036364 9.29E-06 3.65E-06 mr1633 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
vg0614036364 NA 2.30E-07 mr1129_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
vg0614036364 2.62E-06 5.07E-09 mr1243_2 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
vg0614036364 NA 3.16E-08 mr1248_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
vg0614036364 NA 1.09E-07 mr1250_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
vg0614036364 NA 9.75E-09 mr1251_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
vg0614036364 NA 7.53E-06 mr1252_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
vg0614036364 NA 4.58E-07 mr1423_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
vg0614036364 NA 8.75E-09 mr1435_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
vg0614036364 NA 1.26E-07 mr1599_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