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

Detailed information for vg0904237248:

Variant ID: vg0904237248 (JBrowse)Variation Type: INDEL
Chromosome: chr09Position: 4237248
Reference Allele: TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGCAlternative Allele: AGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC,T
Primary Allele: AGTCAGCGTGACTCTGGCGC CTGCACCTTGAAGGTTGAGG GAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGT CGGCSecondary Allele: TGTCAGCGTGACTCTGGCGC CTGCACCTTGAAGGTTGAGG GAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGT CGGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCGCCCTCAATCCCGCGAGGAGTCCTTCGTATTCCGCCATGTTGTTCGTGGCTCGGAAGTCGAGCCAAATGACATACTTGAGGACGTCCCCGCTTGGCGA[TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC/AGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC,T]
GTTTGGGTCCTTTACATCTCTGGGGAGGAAGGAGACGTTGGGTGGAACAGGTTCGTCCACTGGGGTCCACTCCGCGATGAAGTTAGCTAGGACCTGGCTT

Reverse complement sequence

AAGCCAGGTCCTAGCTAACTTCATCGCGGAGTGGACCCCAGTGGACGAACCTGTTCCACCCAACGTCTCCTTCCTCCCCAGAGATGTAAAGGACCCAAAC[GCCGACATTCATGGCGGGCACTGGGTTATGCATTTCGACGGCTCCCTCAACCTTCAAGGTGCAGGCGCCAGAGTCACGCTGACA/GCCGACATTCATGGCGGGCACTGGGTTATGCATTTCGACGGCTCCCTCAACCTTCAAGGTGCAGGCGCCAGAGTCACGCTGACT,A]
TCGCCAAGCGGGGACGTCCTCAAGTATGTCATTTGGCTCGACTTCCGAGCCACGAACAACATGGCGGAATACGAAGGACTCCTCGCGGGATTGAGGGCGG

Allele Frequencies:

Populations Population SizeFrequency of AGTCAGCGTGACTCTGGCGC CTGCACCTTGAAGGTTGAGG GAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGT CGGC(primary allele) Frequency of TGTCAGCGTGACTCTGGCGC CTGCACCTTGAAGGTTGAGG GAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGT CGGC(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.90% 29.20% 10.71% 8.23% T: 0.02%
All Indica  2759 80.60% 2.60% 12.72% 4.02% T: 0.04%
All Japonica  1512 1.30% 83.20% 0.26% 15.21% NA
Aus  269 45.70% 1.90% 52.42% 0.00% NA
Indica I  595 87.10% 5.20% 5.71% 1.85% T: 0.17%
Indica II  465 85.60% 1.50% 9.68% 3.23% NA
Indica III  913 73.10% 1.00% 19.39% 6.57% NA
Indica Intermediate  786 81.70% 3.10% 12.09% 3.18% NA
Temperate Japonica  767 1.20% 79.50% 0.26% 19.04% NA
Tropical Japonica  504 1.20% 95.60% 0.00% 3.17% NA
Japonica Intermediate  241 2.10% 68.90% 0.83% 28.22% NA
VI/Aromatic  96 45.80% 8.30% 3.12% 42.71% NA
Intermediate  90 44.40% 40.00% 7.78% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0904237248 TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC -> AGTCAGCGTGACTCTGGCGCCTGCACCTTG AAGGTTGAGGGAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGTCGGC LOC_Os09g08180.1 synonymous_variant ; p.Thr1859Thr; LOW synonymous_codon Average:44.384; most accessible tissue: Zhenshan97 flag leaf, score: 82.17 N N N N
vg0904237248 TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC -> AGTCAGCGTGACTCTGGCGCCTGCACCTTG AAGGTTGAGGGAGCCGTCGAAATGCATAAC CCAGTGCCCGCCATGAATGTCGGC LOC_Os09g08180.1 synonymous_variant ; p.Thr1859Thr; LOW nonsynonymous_codon ; T1859I Average:44.384; most accessible tissue: Zhenshan97 flag leaf, score: 82.17 unknown unknown unknown unknown
vg0904237248 TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC -> T LOC_Os09g08180.1 frameshift_variant ; p.Ala1832fs; HIGH frameshift_variant Average:44.384; most accessible tissue: Zhenshan97 flag leaf, score: 82.17 N N N N
vg0904237248 TGTCAGCGTGACTCTGGCGCCTGCACCTTGAAGGTTGAGGGAGCCGTCGAAATGCATAACCCAGTGCCCGCCATGAATGTCGGC -> DEL LOC_Os09g08180.1 N frameshift_variant Average:44.384; most accessible tissue: Zhenshan97 flag leaf, score: 82.17 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904237248 4.52E-07 NA Plant_height All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0904237248 2.50E-08 NA Plant_height Jap_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0904237248 NA 1.31E-14 mr1062 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
vg0904237248 NA 5.31E-12 mr1170 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
vg0904237248 NA 2.96E-09 mr1322 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
vg0904237248 NA 5.89E-07 mr1527 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
vg0904237248 NA 4.89E-06 mr1532 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
vg0904237248 NA 8.71E-11 mr1553 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
vg0904237248 NA 4.46E-11 mr1623 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
vg0904237248 NA 2.28E-08 mr1644 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
vg0904237248 NA 5.65E-08 mr1690 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
vg0904237248 NA 2.36E-12 mr1744 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
vg0904237248 6.09E-06 6.09E-06 mr1935 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
vg0904237248 NA 4.12E-21 mr1010_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
vg0904237248 NA 2.09E-18 mr1168_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
vg0904237248 NA 9.75E-07 mr1321_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
vg0904237248 NA 7.52E-06 mr1355_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
vg0904237248 NA 3.00E-10 mr1576_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
vg0904237248 NA 3.50E-12 mr1666_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
vg0904237248 5.98E-06 1.48E-24 mr1698_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
vg0904237248 NA 3.85E-17 mr1712_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
vg0904237248 NA 5.64E-11 mr1761_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
vg0904237248 NA 1.01E-07 mr1765_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
vg0904237248 NA 1.28E-18 mr1817_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
vg0904237248 NA 5.13E-06 mr1875_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