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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1011512046:

Variant ID: vg1011512046 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 11512046
Reference Allele: TCTCGCAAGGAACTCAACCAlternative Allele: ACTCGCAAGGAACTCAACC,CCTCGCAAGGAACTCAACC,T
Primary Allele: TCTCGCAAGGAACTCAACCSecondary Allele: CCTCGCAAGGAACTCAACC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAGCAATACGCCAAGAAGGCACGGAAGCCGACTGATGGAGAACAAAGCACTTCAAAAAAGAAGGATGATGACTATGACGGATCGACTGGTTTTCAAGAC[TCTCGCAAGGAACTCAACC/ACTCGCAAGGAACTCAACC,CCTCGCAAGGAACTCAACC,T]
ATATTTTCGGTGGACCCGAAGCTTACGAGTCCAAGCGGAAGCAAAAGTTGACTGAAAGGGAGATTAACGCCGTCCAGCCCGATACACCCCAATATCTTCG

Reverse complement sequence

CGAAGATATTGGGGTGTATCGGGCTGGACGGCGTTAATCTCCCTTTCAGTCAACTTTTGCTTCCGCTTGGACTCGTAAGCTTCGGGTCCACCGAAAATAT[GGTTGAGTTCCTTGCGAGA/GGTTGAGTTCCTTGCGAGT,GGTTGAGTTCCTTGCGAGG,A]
GTCTTGAAAACCAGTCGATCCGTCATAGTCATCATCCTTCTTTTTTGAAGTGCTTTGTTCTCCATCAGTCGGCTTCCGTGCCTTCTTGGCGTATTGCTCT

Allele Frequencies:

Populations Population SizeFrequency of TCTCGCAAGGAACTCAACC(primary allele) Frequency of CCTCGCAAGGAACTCAACC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 67.60% 8.10% 2.16% 17.58% ACTCGCAAGGAACTCAACC: 4.46%; T: 0.02%
All Indica  2759 72.10% 6.70% 2.25% 15.48% ACTCGCAAGGAACTCAACC: 3.52%
All Japonica  1512 66.70% 12.80% 1.39% 14.88% ACTCGCAAGGAACTCAACC: 4.23%; T: 0.07%
Aus  269 20.80% 0.70% 5.95% 58.36% ACTCGCAAGGAACTCAACC: 14.13%
Indica I  595 86.60% 6.10% 1.34% 6.05% NA
Indica II  465 89.70% 1.50% 2.37% 6.24% ACTCGCAAGGAACTCAACC: 0.22%
Indica III  913 53.80% 9.40% 1.97% 27.71% ACTCGCAAGGAACTCAACC: 7.12%
Indica Intermediate  786 71.90% 7.10% 3.18% 13.87% ACTCGCAAGGAACTCAACC: 3.94%
Temperate Japonica  767 88.30% 0.40% 0.65% 8.87% ACTCGCAAGGAACTCAACC: 1.69%; T: 0.13%
Tropical Japonica  504 45.00% 34.10% 1.59% 11.11% ACTCGCAAGGAACTCAACC: 8.13%
Japonica Intermediate  241 43.20% 7.50% 3.32% 41.91% ACTCGCAAGGAACTCAACC: 4.15%
VI/Aromatic  96 83.30% 1.00% 2.08% 6.25% ACTCGCAAGGAACTCAACC: 7.29%
Intermediate  90 72.20% 3.30% 1.11% 17.78% ACTCGCAAGGAACTCAACC: 5.56%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1011512046 TCTCGCAAGGAACTCAACC -> DEL LOC_Os10g22240.1 N frameshift_variant Average:28.379; most accessible tissue: Callus, score: 42.027 N N N N
vg1011512046 TCTCGCAAGGAACTCAACC -> ACTCGCAAGGAACTCAACC LOC_Os10g22240.1 missense_variant ; p.Ser548Thr; MODERATE nonsynonymous_codon ; S548T Average:28.379; most accessible tissue: Callus, score: 42.027 benign +1.235 N N
vg1011512046 TCTCGCAAGGAACTCAACC -> T LOC_Os10g22240.1 disruptive_inframe_deletion ; p.Ser548_His554delinsTyr; MODERATE inframe_variant Average:28.379; most accessible tissue: Callus, score: 42.027 N N N N
vg1011512046 TCTCGCAAGGAACTCAACC -> CCTCGCAAGGAACTCAACC LOC_Os10g22240.1 missense_variant ; p.Ser548Pro; MODERATE nonsynonymous_codon ; S548P Average:28.379; most accessible tissue: Callus, score: 42.027 benign +0.288 N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1011512046 4.27E-09 1.76E-12 mr1016 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
vg1011512046 9.05E-06 NA mr1017 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
vg1011512046 3.81E-08 5.23E-11 mr1017 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
vg1011512046 6.34E-06 NA mr1018 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
vg1011512046 5.16E-08 2.46E-11 mr1019 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
vg1011512046 7.80E-07 NA mr1055 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
vg1011512046 3.88E-09 4.52E-12 mr1055 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
vg1011512046 NA 6.01E-07 mr1083 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
vg1011512046 5.31E-06 5.31E-06 mr1085 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
vg1011512046 3.62E-07 2.14E-10 mr1132 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
vg1011512046 NA 5.92E-06 mr1364 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
vg1011512046 4.01E-07 NA mr1390 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
vg1011512046 NA 3.06E-06 mr1408 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
vg1011512046 2.95E-07 NA mr1490 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
vg1011512046 NA 4.97E-06 mr1557 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
vg1011512046 NA 8.58E-06 mr1606 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
vg1011512046 NA 6.49E-06 mr1682 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
vg1011512046 4.39E-06 NA mr1055_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
vg1011512046 5.04E-07 NA mr1055_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
vg1011512046 9.04E-08 NA mr1132_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
vg1011512046 1.93E-08 NA mr1390_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
vg1011512046 1.79E-08 NA mr1490_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