Variant ID: vg0909067656 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 9067656 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGCTTTTGATGATTACTGCAGGAAGGAAGGCATCGTTAGGCATCACACCATCCCGTACACTCCACAGCAGAATGGTGTGGCTGAGCGCATGAATAGAACC[A/G]
TCATCTCCAAGGCTCGTTGTATGCTGTCCAACGCTCGCATGAGCAAGCGTTTTTGGGCAGAGGCTACTAACACCGCCTGCTACTTAATCAACAGGTCGCC
GGCGACCTGTTGATTAAGTAGCAGGCGGTGTTAGTAGCCTCTGCCCAAAAACGCTTGCTCATGCGAGCGTTGGACAGCATACAACGAGCCTTGGAGATGA[T/C]
GGTTCTATTCATGCGCTCAGCCACACCATTCTGCTGTGGAGTGTACGGGATGGTGTGATGCCTAACGATGCCTTCCTTCCTGCAGTAATCATCAAAAGCA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 96.50% | 3.50% | 0.00% | 0.00% | NA |
All Indica | 2759 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 74.70% | 25.30% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0909067656 | A -> G | LOC_Os09g15030.1 | missense_variant ; p.Ile368Val; MODERATE | nonsynonymous_codon ; I368V | Average:19.944; most accessible tissue: Zhenshan97 panicle, score: 39.652 | unknown | unknown | TOLERATED | 0.17 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0909067656 | NA | 6.49E-08 | mr1280 | 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 |
vg0909067656 | 3.58E-06 | 3.58E-06 | mr1297 | 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 |
vg0909067656 | NA | 5.91E-06 | mr1510 | 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 |
vg0909067656 | NA | 7.25E-06 | mr1788 | 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 |
vg0909067656 | NA | 4.45E-06 | mr1702_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 |