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Detailed information for vg0615347149:

Variant ID: vg0615347149 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15347149
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGTACTGCCTTAGCCCATCGAAGGCGGCTTGACACTCAGGTGTCCAATTGAGTTTGCCGGCCCCTTGGAGCATCTTGAAAAATGATAAATCTCTTTCGG[T/C]
TGCTCTTGGGAGCAACTCCTTAACTCATTTTCGCCCCTAGCCCTTGTCGCCGTACCTCGCTGGTACTGTGGCGAAAGGCGTGGGTGTGGCGAAACCTGTT

Reverse complement sequence

AACAGGTTTCGCCACACCCACGCCTTTCGCCACAGTACCAGCGAGGTACGGCGACAAGGGCTAGGGGCGAAAATGAGTTAAGGAGTTGCTCCCAAGAGCA[A/G]
CCGAAAGAGATTTATCATTTTTCAAGATGCTCCAAGGGGCCGGCAAACTCAATTGGACACCTGAGTGTCAAGCCGCCTTCGATGGGCTAAGGCAGTACCT

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 64.40% 28.90% 2.37% 4.34% NA
All Indica  2759 96.80% 2.90% 0.25% 0.04% NA
All Japonica  1512 9.10% 82.60% 1.52% 6.75% NA
Aus  269 33.10% 2.20% 28.62% 36.06% NA
Indica I  595 95.30% 4.20% 0.50% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.20% 0.51% 0.13% NA
Temperate Japonica  767 3.80% 80.20% 3.00% 13.04% NA
Tropical Japonica  504 17.70% 82.10% 0.00% 0.20% NA
Japonica Intermediate  241 8.30% 91.30% 0.00% 0.41% NA
VI/Aromatic  96 95.80% 1.00% 2.08% 1.04% NA
Intermediate  90 60.00% 32.20% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0615347149 T -> C LOC_Os06g26234.1 intron_variant ; MODIFIER silent_mutation Average:37.849; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0615347149 T -> C LOC_Os06g26234.2 intron_variant ; MODIFIER silent_mutation Average:37.849; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0615347149 T -> C LOC_Os06g26234.3 intron_variant ; MODIFIER silent_mutation Average:37.849; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg0615347149 T -> DEL N N silent_mutation Average:37.849; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615347149 7.84E-06 7.84E-06 mr1275 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
vg0615347149 NA 2.99E-06 mr1020_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
vg0615347149 NA 7.34E-18 mr1062_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
vg0615347149 NA 4.85E-06 mr1153_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
vg0615347149 NA 4.32E-08 mr1165_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
vg0615347149 1.18E-06 NA mr1172_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
vg0615347149 NA 5.94E-07 mr1275_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
vg0615347149 NA 1.20E-07 mr1302_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
vg0615347149 NA 2.84E-07 mr1405_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
vg0615347149 NA 1.58E-09 mr1478_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
vg0615347149 NA 8.06E-06 mr1574_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
vg0615347149 NA 1.94E-08 mr1660_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
vg0615347149 NA 5.22E-08 mr1668_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
vg0615347149 NA 6.34E-12 mr1714_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
vg0615347149 8.54E-07 2.82E-10 mr1765_2 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
vg0615347149 NA 6.85E-12 mr1781_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
vg0615347149 1.71E-06 1.71E-06 mr1971_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
vg0615347149 NA 4.11E-11 mr1986_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