Variant ID: vg1003777399 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 3777399 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )
TCGAAGAAGAAACCAAAGCACTAGAATTAGAATCAACTTTACGAGAAAGAATATTCATCTCATGTGTTTTGAGTTTTGTGTAAAGCGAATCCAAAGTCAA[C/A]
GTAGACATATCAACAGACTCTTGAATTGATGTAACTTTCATCTCCCAAATAGACATGTCAAGACCATTCAAAAAATGACGAGAAACCTTAGATTGTGTGT
ACACACAATCTAAGGTTTCTCGTCATTTTTTGAATGGTCTTGACATGTCTATTTGGGAGATGAAAGTTACATCAATTCAAGAGTCTGTTGATATGTCTAC[G/T]
TTGACTTTGGATTCGCTTTACACAAAACTCAAAACACATGAGATGAATATTCTTTCTCGTAAAGTTGATTCTAATTCTAGTGCTTTGGTTTCTTCTTCGA
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 75.30% | 15.30% | 6.90% | 2.54% | NA |
All Indica | 2759 | 60.20% | 25.90% | 10.87% | 3.04% | NA |
All Japonica | 1512 | 96.40% | 0.10% | 1.12% | 2.31% | NA |
Aus | 269 | 98.50% | 0.00% | 1.49% | 0.00% | NA |
Indica I | 595 | 66.10% | 23.70% | 7.90% | 2.35% | NA |
Indica II | 465 | 64.10% | 23.20% | 9.68% | 3.01% | NA |
Indica III | 913 | 49.20% | 32.30% | 15.22% | 3.29% | NA |
Indica Intermediate | 786 | 66.30% | 21.60% | 8.78% | 3.31% | NA |
Temperate Japonica | 767 | 99.30% | 0.10% | 0.13% | 0.39% | NA |
Tropical Japonica | 504 | 91.70% | 0.00% | 2.98% | 5.36% | NA |
Japonica Intermediate | 241 | 97.10% | 0.40% | 0.41% | 2.07% | NA |
VI/Aromatic | 96 | 95.80% | 0.00% | 4.17% | 0.00% | NA |
Intermediate | 90 | 91.10% | 6.70% | 1.11% | 1.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1003777399 | C -> A | LOC_Os10g07190.1 | synonymous_variant ; p.Thr184Thr; LOW | synonymous_codon | Average:6.591; most accessible tissue: Callus, score: 12.183 | N | N | N | N |
vg1003777399 | C -> DEL | LOC_Os10g07190.1 | N | frameshift_variant | Average:6.591; most accessible tissue: Callus, score: 12.183 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1003777399 | 9.02E-07 | 2.05E-06 | mr1632 | Ind_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 |
vg1003777399 | 1.31E-06 | 3.62E-07 | mr1514_2 | Ind_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 |