Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0620831120:

Variant ID: vg0620831120 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 20831120
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGCTTTTTCAACCAAGGCAGGTCAAGGGTCCAAGAGCCTTATCCTTCGAAAACGATTCTCCGACGACAAGGCTGGGGGCTATGGAGAGCGTATGACTCAA[C/T]
AAACTGACTGATCGAAGTCGGTAAGAAAGAAGATGCTCGTACACAAAACATTAGTCTGTAAATTTAATTCATTTTTAGTTTTCCATACATATTATAACAT

Reverse complement sequence

ATGTTATAATATGTATGGAAAACTAAAAATGAATTAAATTTACAGACTAATGTTTTGTGTACGAGCATCTTCTTTCTTACCGACTTCGATCAGTCAGTTT[G/A]
TTGAGTCATACGCTCTCCATAGCCCCCAGCCTTGTCGTCGGAGAATCGTTTTCGAAGGATAAGGCTCTTGGACCCTTGACCTGCCTTGGTTGAAAAAGCA

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 97.00% 1.90% 0.13% 0.95% NA
All Indica  2759 99.90% 0.00% 0.04% 0.04% NA
All Japonica  1512 91.10% 5.80% 0.33% 2.78% NA
Aus  269 100.00% 0.00% 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% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.00% 0.13% NA
Temperate Japonica  767 92.00% 7.20% 0.13% 0.65% NA
Tropical Japonica  504 98.80% 0.00% 0.00% 1.19% NA
Japonica Intermediate  241 72.20% 13.30% 1.66% 12.86% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 3.30% 0.00% 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
vg0620831120 C -> T LOC_Os06g35690.1 downstream_gene_variant ; 1276.0bp to feature; MODIFIER silent_mutation Average:45.693; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N
vg0620831120 C -> T LOC_Os06g35700.1 downstream_gene_variant ; 1312.0bp to feature; MODIFIER silent_mutation Average:45.693; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N
vg0620831120 C -> T LOC_Os06g35690-LOC_Os06g35700 intergenic_region ; MODIFIER silent_mutation Average:45.693; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N
vg0620831120 C -> DEL N N silent_mutation Average:45.693; most accessible tissue: Zhenshan97 root, score: 75.661 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0620831120 4.98E-06 1.96E-06 mr1037_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
vg0620831120 NA 2.05E-07 mr1827_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
vg0620831120 4.00E-06 4.30E-08 mr1842_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