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Detailed information for vg0813085446:

Variant ID: vg0813085446 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 13085446
Reference Allele: TAlternative Allele: G,A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGGCATAGGCTACCACATGACCTTCCTGCATTAATACGCACCCCAATCCTTGGCGCGAAGCGTCACAGTACACCAGGAAGTCCTTGCGAGTATCCGGTA[T/G,A]
GATTAGCACTGGCGAGGAAACCAGCTTTTCTTTGAGAGTTTGGAATGCTTTCTCGCATTGAGGGCTCCACACAAATTTTTCTTCCTTCTTCAGCAACTGC

Reverse complement sequence

GCAGTTGCTGAAGAAGGAAGAAAAATTTGTGTGGAGCCCTCAATGCGAGAAAGCATTCCAAACTCTCAAAGAAAAGCTGGTTTCCTCGCCAGTGCTAATC[A/C,T]
TACCGGATACTCGCAAGGACTTCCTGGTGTACTGTGACGCTTCGCGCCAAGGATTGGGGTGCGTATTAATGCAGGAAGGTCATGTGGTAGCCTATGCCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.60% 1.60% 28.78% 22.94% G: 0.04%
All Indica  2759 14.50% 2.40% 46.43% 36.64% G: 0.07%
All Japonica  1512 94.20% 0.10% 2.71% 2.91% NA
Aus  269 84.40% 2.20% 8.92% 4.46% NA
Indica I  595 6.90% 2.20% 42.18% 48.74% NA
Indica II  465 10.50% 2.20% 42.15% 45.16% NA
Indica III  913 20.30% 3.50% 53.89% 22.23% G: 0.11%
Indica Intermediate  786 15.90% 1.30% 43.51% 39.19% G: 0.13%
Temperate Japonica  767 95.40% 0.00% 1.83% 2.74% NA
Tropical Japonica  504 94.60% 0.40% 2.78% 2.18% NA
Japonica Intermediate  241 89.60% 0.00% 5.39% 4.98% NA
VI/Aromatic  96 97.90% 0.00% 1.04% 1.04% NA
Intermediate  90 64.40% 3.30% 14.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0813085446 T -> G LOC_Os08g21860.1 missense_variant ; p.Ile1081Leu; MODERATE nonsynonymous_codon ; I1081L Average:8.943; most accessible tissue: Callus, score: 23.207 possibly damaging -1.545 TOLERATED 1.00
vg0813085446 T -> A LOC_Os08g21860.1 missense_variant ; p.Ile1081Leu; MODERATE nonsynonymous_codon ; I1081L Average:8.943; most accessible tissue: Callus, score: 23.207 possibly damaging -1.545 TOLERATED 1.00
vg0813085446 T -> DEL LOC_Os08g21860.1 N frameshift_variant Average:8.943; most accessible tissue: Callus, score: 23.207 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0813085446 9.50E-06 NA mr1080 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
vg0813085446 8.22E-06 NA mr1203 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
vg0813085446 NA 9.27E-08 mr1238 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
vg0813085446 NA 3.83E-14 mr1270 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
vg0813085446 2.98E-06 4.63E-08 mr1309 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
vg0813085446 NA 1.86E-07 mr1321 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
vg0813085446 NA 3.85E-09 mr1342 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
vg0813085446 NA 2.24E-29 mr1426 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
vg0813085446 NA 2.12E-09 mr1457 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
vg0813085446 NA 5.61E-16 mr1484 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
vg0813085446 NA 7.36E-18 mr1566 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
vg0813085446 7.36E-06 7.36E-06 mr1566 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
vg0813085446 NA 1.72E-11 mr1609 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
vg0813085446 2.92E-06 3.21E-06 mr1619 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
vg0813085446 NA 1.05E-06 mr1756 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
vg0813085446 NA 5.62E-26 mr1841 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
vg0813085446 7.15E-06 1.61E-09 mr1841 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
vg0813085446 NA 6.59E-25 mr1862 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
vg0813085446 NA 1.46E-13 mr1883 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
vg0813085446 1.41E-08 1.41E-08 mr1900 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
vg0813085446 NA 1.61E-13 mr1914 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
vg0813085446 NA 1.93E-11 mr1938 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
vg0813085446 NA 6.59E-11 mr1945 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
vg0813085446 NA 1.32E-06 mr1841_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