Variant ID: vg0216113702 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 16113702 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )
GCCAAATTTCTACAGAAGGTATGTCTGTTGGATTATCTGGTGTGAAGGTATGGTTGTTGTTTGCTCTCACTTTGGTGCGGTTCCGTGGATTGGTGACCAC[G/A]
TATTATGCAAAGTTCTAGAGATTTTCACCTGATGTGCATTATTTTGATGGTATGACTACTGGGAATAGTGTGTTGTGGGAACCTAAACTATTGCCACTGT
ACAGTGGCAATAGTTTAGGTTCCCACAACACACTATTCCCAGTAGTCATACCATCAAAATAATGCACATCAGGTGAAAATCTCTAGAACTTTGCATAATA[C/T]
GTGGTCACCAATCCACGGAACCGCACCAAAGTGAGAGCAAACAACAACCATACCTTCACACCAGATAATCCAACAGACATACCTTCTGTAGAAATTTGGC
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 | 97.10% | 2.10% | 0.80% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 91.30% | 6.20% | 2.45% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 83.80% | 11.90% | 4.30% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 97.10% | 1.20% | 1.66% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0216113702 | G -> A | LOC_Os02g27360.1 | downstream_gene_variant ; 1195.0bp to feature; MODIFIER | silent_mutation | Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0216113702 | G -> A | LOC_Os02g27360.2 | downstream_gene_variant ; 1195.0bp to feature; MODIFIER | silent_mutation | Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0216113702 | G -> A | LOC_Os02g27350.1 | intron_variant ; MODIFIER | silent_mutation | Average:57.906; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0216113702 | NA | 8.33E-07 | mr1028 | 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 |
vg0216113702 | 1.50E-07 | 1.50E-07 | mr1369 | 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 |
vg0216113702 | 3.80E-06 | 3.80E-06 | mr1373 | 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 |
vg0216113702 | NA | 6.97E-07 | mr1453 | 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 |
vg0216113702 | NA | 6.79E-08 | mr1652 | 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 |
vg0216113702 | NA | 3.13E-06 | mr1697 | 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 |