Variant ID: vg0808191687 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 8191687 |
Reference Allele: A | Alternative Allele: C |
Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGTACCCGCTCGCGATGATGTACTTGTCCGTGAACTCGCGCCACAGCTCGTTGTGCTCCAACGACTCCTCCTCCTCTGCTTTCTTGATCGCATCTTCCTC[A/C]
TCATCATCATCATCATCTGAATCGTCGGCGTACTCCGGTCGGTGATGACAGCCACAGGTGGTAGAGGAATCACGGTGGTCGGAGGAGGAGTCGCCGCCGC
GCGGCGGCGACTCCTCCTCCGACCACCGTGATTCCTCTACCACCTGTGGCTGTCATCACCGACCGGAGTACGCCGACGATTCAGATGATGATGATGATGA[T/G]
GAGGAAGATGCGATCAAGAAAGCAGAGGAGGAGGAGTCGTTGGAGCACAACGAGCTGTGGCGCGAGTTCACGGACAAGTACATCATCGCGAGCGGGTACG
Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 92.90% | 6.90% | 0.23% | 0.00% | NA |
All Indica | 2759 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 89.40% | 9.90% | 0.73% | 0.00% | NA |
Aus | 269 | 53.20% | 46.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 95.30% | 3.30% | 1.43% | 0.00% | NA |
Tropical Japonica | 504 | 81.00% | 19.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 88.40% | 11.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 88.90% | 11.10% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0808191687 | A -> C | LOC_Os08g13740.1 | missense_variant ; p.Asp189Glu; MODERATE | nonsynonymous_codon ; D189E | Average:55.549; most accessible tissue: Zhenshan97 young leaf, score: 82.077 | unknown | unknown | TOLERATED | 0.44 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0808191687 | NA | 5.16E-06 | mr1057 | 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 |
vg0808191687 | NA | 9.47E-07 | mr1345 | 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 |
vg0808191687 | NA | 4.70E-06 | mr1417 | 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 |
vg0808191687 | 6.03E-06 | NA | mr1757 | 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 |
vg0808191687 | 1.89E-07 | NA | mr1549_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 |
vg0808191687 | 1.62E-07 | NA | mr1757_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 |