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Detailed information for vg0106805757:

Variant ID: vg0106805757 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 6805757
Reference Allele: TATATATAGGTATTAAlternative Allele: GATATATAGGTATTA,T,AATATATAGGTATTA,TAGATATATAGGTATTA
Primary Allele: TATATATAGGTATTASecondary Allele: GATATATAGGTATTA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGGGTTATTTAAGGGCTAAGTTCCTAATTTAAAAAGGTTGAATATATCCGTTTGGATGTAGAGGCCGGGTAAAAATACCATTCTCTCTCTCTATATATA[TATATATAGGTATTA/GATATATAGGTATTA,T,AATATATAGGTATTA,TAGATATATAGGTATTA]
TTCTCTCTCCTTTTCAAAGTATGATGATGAGGTAGATCTAACTGTGAAATTATCAAGAGAAAATTAATAAAGGTTTAGTTTTCAAATTTGCTAGTGCTGC

Reverse complement sequence

GCAGCACTAGCAAATTTGAAAACTAAACCTTTATTAATTTTCTCTTGATAATTTCACAGTTAGATCTACCTCATCATCATACTTTGAAAAGGAGAGAGAA[TAATACCTATATATA/TAATACCTATATATC,A,TAATACCTATATATT,TAATACCTATATATCTA]
TATATATAGAGAGAGAGAATGGTATTTTTACCCGGCCTCTACATCCAAACGGATATATTCAACCTTTTTAAATTAGGAACTTAGCCCTTAAATAACCCAA

Allele Frequencies:

Populations Population SizeFrequency of TATATATAGGTATTA(primary allele) Frequency of GATATATAGGTATTA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.90% 9.00% 5.42% 13.52% AATATATAGGTATTA: 0.83%; T: 0.28%; TAGATATATAGGTATTA: 0.02%
All Indica  2759 70.80% 1.60% 5.84% 20.91% T: 0.47%; AATATATAGGTATTA: 0.43%
All Japonica  1512 74.10% 24.50% 0.33% 0.99% TAGATATATAGGTATTA: 0.07%; AATATATAGGTATTA: 0.07%
Aus  269 58.40% 1.10% 23.79% 10.04% AATATATAGGTATTA: 6.69%
Indica I  595 87.40% 0.00% 2.69% 9.58% T: 0.34%
Indica II  465 52.30% 0.90% 10.75% 35.48% T: 0.43%; AATATATAGGTATTA: 0.22%
Indica III  913 80.50% 1.00% 4.49% 12.49% T: 0.88%; AATATATAGGTATTA: 0.66%
Indica Intermediate  786 57.80% 3.90% 6.87% 30.66% AATATATAGGTATTA: 0.64%; T: 0.13%
Temperate Japonica  767 96.60% 1.70% 0.26% 1.43% NA
Tropical Japonica  504 46.00% 53.00% 0.40% 0.40% TAGATATATAGGTATTA: 0.20%
Japonica Intermediate  241 61.00% 37.30% 0.41% 0.83% AATATATAGGTATTA: 0.41%
VI/Aromatic  96 69.80% 0.00% 18.75% 3.12% AATATATAGGTATTA: 8.33%
Intermediate  90 61.10% 11.10% 8.89% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106805757 TATATATAGGTATTA -> T LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:61.146; most accessible tissue: Zhenshan97 flower, score: 88.357 N N N N
vg0106805757 TATATATAGGTATTA -> GATATATAGGTATTA LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:61.146; most accessible tissue: Zhenshan97 flower, score: 88.357 N N N N
vg0106805757 TATATATAGGTATTA -> DEL N N silent_mutation Average:61.146; most accessible tissue: Zhenshan97 flower, score: 88.357 N N N N
vg0106805757 TATATATAGGTATTA -> AATATATAGGTATTA LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:61.146; most accessible tissue: Zhenshan97 flower, score: 88.357 N N N N
vg0106805757 TATATATAGGTATTA -> TAGATATATAGGTATTA LOC_Os01g12430-LOC_Os01g12440 intergenic_region ; MODIFIER silent_mutation Average:61.146; most accessible tissue: Zhenshan97 flower, score: 88.357 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106805757 NA 2.22E-10 mr1017 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
vg0106805757 NA 1.68E-09 mr1022 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
vg0106805757 NA 6.73E-11 mr1055 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
vg0106805757 5.67E-07 6.80E-10 mr1236 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
vg0106805757 1.54E-06 2.34E-11 mr1236 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
vg0106805757 1.54E-10 1.08E-08 mr1498 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
vg0106805757 NA 5.88E-09 mr1518 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
vg0106805757 7.92E-07 9.55E-20 mr1676 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
vg0106805757 NA 1.38E-10 mr1676 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
vg0106805757 9.62E-26 5.05E-31 mr1769 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
vg0106805757 6.30E-22 1.17E-41 mr1769 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
vg0106805757 7.92E-06 NA mr1778 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
vg0106805757 1.67E-06 NA mr1916 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
vg0106805757 NA 3.11E-08 mr1916 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
vg0106805757 2.94E-09 1.94E-07 mr1925 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
vg0106805757 3.08E-06 3.00E-08 mr1925 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
vg0106805757 1.01E-11 2.05E-16 mr1951 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
vg0106805757 4.41E-09 4.32E-17 mr1951 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
vg0106805757 NA 2.15E-07 mr1236_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
vg0106805757 NA 1.62E-06 mr1236_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
vg0106805757 7.26E-16 5.71E-13 mr1498_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
vg0106805757 6.35E-14 8.19E-17 mr1498_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
vg0106805757 2.46E-06 8.24E-21 mr1676_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
vg0106805757 NA 7.03E-11 mr1676_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
vg0106805757 7.51E-36 1.40E-43 mr1769_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
vg0106805757 2.43E-31 1.06E-58 mr1769_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
vg0106805757 1.97E-08 2.68E-25 mr1916_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
vg0106805757 NA 1.54E-13 mr1916_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
vg0106805757 6.35E-09 NA mr1925_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
vg0106805757 9.23E-11 1.72E-11 mr1951_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
vg0106805757 6.88E-09 4.85E-10 mr1951_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