Variant ID: vg0711409773 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 11409773 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 195. )
TGGATAAGCCGAGTCGAGTAATAAAACATTGTTGAAATTGTCGTTTTGCCAGTTGAGGTAAATCTTGGCTCTCTTCGGTATTTCAAGCAAGACGACTTGT[T/C]
AGTTGAAGATTACAAGACCTTGATGGGAAGCAATTTTGAAGACGTCATCGACAAGCGTTTGCAGACTTTGAAGGAGATGAAGGCACTTCAAGATGGTGTT
AACACCATCTTGAAGTGCCTTCATCTCCTTCAAAGTCTGCAAACGCTTGTCGATGACGTCTTCAAAATTGCTTCCCATCAAGGTCTTGTAATCTTCAACT[A/G]
ACAAGTCGTCTTGCTTGAAATACCGAAGAGAGCCAAGATTTACCTCAACTGGCAAAACGACAATTTCAACAATGTTTTATTACTCGACTCGGCTTATCCA
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 27.80% | 21.90% | 2.37% | 47.84% | NA |
All Indica | 2759 | 5.00% | 18.60% | 2.46% | 73.90% | NA |
All Japonica | 1512 | 74.50% | 24.00% | 0.13% | 1.32% | NA |
Aus | 269 | 4.10% | 21.90% | 14.13% | 59.85% | NA |
Indica I | 595 | 5.20% | 33.10% | 1.34% | 60.34% | NA |
Indica II | 465 | 9.20% | 10.80% | 4.30% | 75.70% | NA |
Indica III | 913 | 2.20% | 6.20% | 3.40% | 88.17% | NA |
Indica Intermediate | 786 | 5.60% | 26.70% | 1.15% | 66.54% | NA |
Temperate Japonica | 767 | 65.60% | 33.10% | 0.26% | 1.04% | NA |
Tropical Japonica | 504 | 85.90% | 13.30% | 0.00% | 0.79% | NA |
Japonica Intermediate | 241 | 79.30% | 17.40% | 0.00% | 3.32% | NA |
VI/Aromatic | 96 | 3.10% | 86.50% | 0.00% | 10.42% | NA |
Intermediate | 90 | 41.10% | 20.00% | 4.44% | 34.44% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0711409773 | T -> DEL | LOC_Os07g19274.1 | N | frameshift_variant | Average:7.325; most accessible tissue: Callus, score: 17.943 | N | N | N | N |
vg0711409773 | T -> C | LOC_Os07g19274.1 | missense_variant ; p.Leu524Ser; MODERATE | nonsynonymous_codon ; L524S | Average:7.325; most accessible tissue: Callus, score: 17.943 | benign | 0.082 | TOLERATED | 1.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0711409773 | NA | 4.79E-09 | Awn_length | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0711409773 | NA | 3.64E-06 | mr1236 | 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 |
vg0711409773 | 1.90E-06 | 1.90E-06 | mr1270 | 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 |
vg0711409773 | 3.00E-06 | 3.00E-06 | mr1575 | Ind_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 |
vg0711409773 | NA | 1.90E-07 | mr1624_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 |