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Detailed information for vg1001363789:

Variant ID: vg1001363789 (JBrowse)Variation Type: INDEL
Chromosome: chr10Position: 1363789
Reference Allele: CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGAAlternative Allele: C,TGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA,CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA
Primary Allele: CGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGASecondary Allele: TGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGCTTTTAAGCCTAGTTATGTTTATGATATCTTTTTTAGATCTCGGAAAGGGTTCTTCATAAAATTGATTATTATAGATCATGTTTCTTTTGACAAGG[CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA/C,TGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA,CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA]
GTTCACAACTTAGAAATTCAAAACCAGTATATGTTGAGTAAATTGTTATTTAAGTTAATTAATGAGCAGGGGGTTTGGCAAGATTTATTGAAAAGGAAAT

Reverse complement sequence

ATTTCCTTTTCAATAAATCTTGCCAAACCCCCTGCTCATTAATTAACTTAAATAACAATTTACTCAACATATACTGGTTTTGAATTTCTAAGTTGTGAAC[TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCG/G,TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCA,TCCAAGACCACCCTGCTCTTTGGGCTGACATATAATGTCTCATCTTGTAAGTATGTACTTCTTTTTAATGCTTATCCCCTCAAAAAAAAATTCTAAGTTGTGAACG]
CCTTGTCAAAAGAAACATGATCTATAATAATCAATTTTATGAAGAACCCTTTCCGAGATCTAAAAAAGATATCATAAACATAACTAGGCTTAAAAGCACA

Allele Frequencies:

Populations Population SizeFrequency of CGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA(primary allele) Frequency of TGATAAGCATTAAAAAGAAG TACATACTTACAAGATGAGA CATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.40% 7.80% 1.16% 0.00% C: 6.60%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.06%
All Indica  2759 73.70% 13.00% 1.92% 0.00% C: 11.24%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.11%
All Japonica  1512 99.70% 0.10% 0.07% 0.00% C: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 73.30% 1.30% 2.86% 0.00% C: 22.35%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.17%
Indica II  465 59.60% 29.20% 2.58% 0.00% C: 8.17%; CGTTCACAACTTAGAATTTTTTTTTGAGGGGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA: 0.43%
Indica III  913 75.70% 14.20% 0.77% 0.00% C: 9.31%
Indica Intermediate  786 80.20% 10.80% 2.16% 0.00% C: 6.87%
Temperate Japonica  767 99.70% 0.10% 0.00% 0.00% C: 0.13%
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 91.10% 6.70% 1.11% 0.00% C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA LOC_Os10g03240.1 upstream_gene_variant ; 2827.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA LOC_Os10g03220.1 downstream_gene_variant ; 4608.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA LOC_Os10g03230.1 downstream_gene_variant ; 3473.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> TGATAAGCATTAAAAAGAAGTACATACTTA CAAGATGAGACATTATATGTCAGCCCAAAG AGCAGGGTGGTCTTGGA LOC_Os10g03230-LOC_Os10g03240 intergenic_region ; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C LOC_Os10g03240.1 upstream_gene_variant ; 2826.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C LOC_Os10g03220.1 downstream_gene_variant ; 4609.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C LOC_Os10g03230.1 downstream_gene_variant ; 3474.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> C LOC_Os10g03230-LOC_Os10g03240 intergenic_region ; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA LOC_Os10g03240.1 upstream_gene_variant ; 2825.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA LOC_Os10g03220.1 downstream_gene_variant ; 4610.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA LOC_Os10g03230.1 downstream_gene_variant ; 3475.0bp to feature; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N
vg1001363789 CGATAAGCATTAAAAAGAAGTACATACTTACAAGATGAGACATTATATGTCAGCCCAAAGAGCAGGGTGGTCTTGGA -> CGTTCACAACTTAGAATTTTTTTTTGAGGG GATAAGCATTAAAAAGAAGTACATACTTAC AAGATGAGACATTATATGTCAGCCCAAAGA GCAGGGTGGTCTTGGA LOC_Os10g03230-LOC_Os10g03240 intergenic_region ; MODIFIER silent_mutation Average:33.503; most accessible tissue: Callus, score: 53.84 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001363789 9.74E-16 NA mr1486 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
vg1001363789 2.32E-18 2.53E-15 mr1486 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
vg1001363789 1.90E-14 NA mr1548 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
vg1001363789 2.29E-14 3.01E-11 mr1548 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
vg1001363789 6.23E-10 NA mr1588 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
vg1001363789 9.55E-12 9.47E-12 mr1588 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
vg1001363789 NA 8.56E-08 mr1158_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
vg1001363789 NA 2.68E-08 mr1158_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
vg1001363789 2.12E-16 NA mr1486_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
vg1001363789 1.12E-19 5.31E-20 mr1486_2 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
vg1001363789 4.81E-14 NA mr1588_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
vg1001363789 1.24E-15 2.05E-16 mr1588_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