Variant ID: vg0710366378 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 10366378 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, C: 0.07, others allele: 0.00, population size: 74. )
GAGGAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAACGAAGAAGAGGGGAATGAGGATCCAAACCAGTACTTGAACGAGGAAG[G/C]
GAACGTGAAGAAGGATGCGGAGGGGAACCAGGAGGGGAACGTGGAGAGGGATGTGGAGGGGAACCAGGAGGAGGAGGCTAGTGGAAGTCAACCCTCCGCT
AGCGGAGGGTTGACTTCCACTAGCCTCCTCCTCCTGGTTCCCCTCCACATCCCTCTCCACGTTCCCCTCCTGGTTCCCCTCCGCATCCTTCTTCACGTTC[C/G]
CTTCCTCGTTCAAGTACTGGTTTGGATCCTCATTCCCCTCTTCTTCGTTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTCCTC
Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 41.30% | 40.60% | 10.66% | 7.51% | NA |
All Indica | 2759 | 67.50% | 8.20% | 13.19% | 11.13% | NA |
All Japonica | 1512 | 0.90% | 95.60% | 0.93% | 2.65% | NA |
Aus | 269 | 13.80% | 62.80% | 22.30% | 1.12% | NA |
Indica I | 595 | 68.10% | 6.90% | 16.13% | 8.91% | NA |
Indica II | 465 | 61.50% | 5.20% | 16.13% | 17.20% | NA |
Indica III | 913 | 75.00% | 4.70% | 9.53% | 10.73% | NA |
Indica Intermediate | 786 | 62.00% | 14.90% | 13.49% | 9.67% | NA |
Temperate Japonica | 767 | 1.00% | 98.00% | 0.65% | 0.26% | NA |
Tropical Japonica | 504 | 0.40% | 91.10% | 1.19% | 7.34% | NA |
Japonica Intermediate | 241 | 1.20% | 97.10% | 1.24% | 0.41% | NA |
VI/Aromatic | 96 | 9.40% | 34.40% | 56.25% | 0.00% | NA |
Intermediate | 90 | 31.10% | 50.00% | 13.33% | 5.56% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0710366378 | G -> DEL | LOC_Os07g17530.1 | N | frameshift_variant | Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638 | N | N | N | N |
vg0710366378 | G -> C | LOC_Os07g17530.1 | missense_variant ; p.Gly914Ala; MODERATE | nonsynonymous_codon ; G914A | Average:23.806; most accessible tissue: Minghui63 young leaf, score: 32.638 | benign | 1.408 | DELETERIOUS | 0.01 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0710366378 | NA | 2.87E-21 | mr1051 | 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 |
vg0710366378 | 2.72E-06 | 4.99E-37 | mr1828 | 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 |