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Detailed information for vg0619961711:

Variant ID: vg0619961711 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 19961711
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTGCCTTTGTAGCCCCCGAGCTGATGTTGGGGGCGACCGGGCTATCTTCGCCGCTTGCCTCTTTCACTGATGGCCTCATCAGGACGTCCAAAAAGGTGC[T/C]
AGTTTCAAGTGGCTCTCATCTGGACGCACGTCGTGCTAGATCATCCGGTTCGATGTTGTCTTTGCGGTATACATGTCGGACCTCGATCCCATCAAACCTT

Reverse complement sequence

AAGGTTTGATGGGATCGAGGTCCGACATGTATACCGCAAAGACAACATCGAACCGGATGATCTAGCACGACGTGCGTCCAGATGAGAGCCACTTGAAACT[A/G]
GCACCTTTTTGGACGTCCTGATGAGGCCATCAGTGAAAGAGGCAAGCGGCGAAGATAGCCCGGTCGCCCCCAACATCAGCTCGGGGGCTACAAAGGCAGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 8.20% 0.80% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 75.70% 23.90% 0.40% 0.00% 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 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 88.00% 11.90% 0.13% 0.00% NA
Tropical Japonica  504 71.60% 28.40% 0.00% 0.00% NA
Japonica Intermediate  241 44.80% 53.10% 2.07% 0.00% NA
VI/Aromatic  96 68.80% 5.20% 26.04% 0.00% NA
Intermediate  90 84.40% 8.90% 6.67% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0619961711 T -> C LOC_Os06g34320.1 3_prime_UTR_variant ; 164.0bp to feature; MODIFIER silent_mutation Average:30.434; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg0619961711 T -> C LOC_Os06g34300.1 upstream_gene_variant ; 4977.0bp to feature; MODIFIER silent_mutation Average:30.434; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N
vg0619961711 T -> C LOC_Os06g34310.1 downstream_gene_variant ; 579.0bp to feature; MODIFIER silent_mutation Average:30.434; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0619961711 9.45E-06 1.67E-06 mr1041 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
vg0619961711 NA 8.16E-06 mr1192 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
vg0619961711 NA 9.63E-07 mr1229 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
vg0619961711 NA 2.65E-06 mr1293 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
vg0619961711 NA 8.57E-07 mr1294 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
vg0619961711 NA 9.77E-09 mr1302 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
vg0619961711 NA 7.67E-08 mr1315 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
vg0619961711 NA 8.43E-07 mr1392 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
vg0619961711 NA 4.16E-07 mr1418 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
vg0619961711 NA 9.50E-07 mr1420 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
vg0619961711 NA 5.86E-08 mr1488 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
vg0619961711 NA 3.76E-08 mr1506 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
vg0619961711 NA 2.84E-07 mr1507 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
vg0619961711 NA 4.01E-07 mr1596 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
vg0619961711 3.35E-07 3.34E-07 mr1597 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
vg0619961711 NA 3.60E-09 mr1604 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
vg0619961711 NA 1.27E-06 mr1622 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
vg0619961711 NA 3.02E-07 mr1677 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
vg0619961711 NA 4.96E-07 mr1764 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
vg0619961711 NA 5.75E-07 mr1809 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
vg0619961711 NA 5.39E-08 mr1810 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
vg0619961711 NA 9.43E-07 mr1886 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
vg0619961711 NA 7.53E-06 mr1906 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