Variant ID: vg1117387081 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 17387081 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 111. )
CGTTGGTGCCATGAGCAGTAGCCTTGCCCAAATCCAATGACCAACTGCACGGGACGCCGCAGCGGTACTTCCCCATTGCCTCCATGCTTGAAATCCCATG[G/A]
ATCAGCGGCTCTGATACCATATTTTTAGCAACCAAATCACCAAACAACAAGAATTTCACCACGAACAACTATCCAGTCAACAGTGCTGTTTTTGGAGGTG
CACCTCCAAAAACAGCACTGTTGACTGGATAGTTGTTCGTGGTGAAATTCTTGTTGTTTGGTGATTTGGTTGCTAAAAATATGGTATCAGAGCCGCTGAT[C/T]
CATGGGATTTCAAGCATGGAGGCAATGGGGAAGTACCGCTGCGGCGTCCCGTGCAGTTGGTCATTGGATTTGGGCAAGGCTACTGCTCATGGCACCAACG
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 77.70% | 21.90% | 0.19% | 0.15% | NA |
All Indica | 2759 | 77.90% | 21.60% | 0.25% | 0.25% | NA |
All Japonica | 1512 | 87.80% | 12.20% | 0.00% | 0.00% | NA |
Aus | 269 | 13.80% | 85.50% | 0.74% | 0.00% | NA |
Indica I | 595 | 77.60% | 22.40% | 0.00% | 0.00% | NA |
Indica II | 465 | 78.10% | 20.90% | 0.43% | 0.65% | NA |
Indica III | 913 | 80.90% | 19.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 74.40% | 24.40% | 0.64% | 0.51% | NA |
Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 68.30% | 31.70% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 77.80% | 22.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1117387081 | G -> A | LOC_Os11g29920.1 | synonymous_variant ; p.Ile956Ile; LOW | synonymous_codon | Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765 | N | N | N | N |
vg1117387081 | G -> DEL | LOC_Os11g29920.1 | N | frameshift_variant | Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1117387081 | 2.39E-06 | NA | mr1017 | 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 |
vg1117387081 | 3.39E-07 | NA | mr1132_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 |
vg1117387081 | 5.60E-06 | NA | mr1390_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 |
vg1117387081 | 2.62E-06 | NA | mr1490_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 |