| Variant ID: vg0707566881 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 7566881 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 97. )
TTCTCGGCCAAGCACTTTTGCTGATAGCCTTTGGCTCGGGGAAGAACAGACGCGAAGAGCAAATACTGTTCGACGTCGTCGACATCCCGTACAACTACAA[T/C]
GCCATCTTTGGCCGTGCAACCCTGAACAAGTTCGAAGCCATTTCCCACCACAATTATCTCAAGCTCAAGATGCCCAGCCCGACAGTGGTGATAGTAGTCA
TGACTACTATCACCACTGTCGGGCTGGGCATCTTGAGCTTGAGATAATTGTGGTGGGAAATGGCTTCGAACTTGTTCAGGGTTGCACGGCCAAAGATGGC[A/G]
TTGTAGTTGTACGGGATGTCGACGACGTCGAACAGTATTTGCTCTTCGCGTCTGTTCTTCCCCGAGCCAAAGGCTATCAGCAAAAGTGCTTGGCCGAGAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.00% | 36.80% | 0.91% | 5.25% | NA |
| All Indica | 2759 | 92.10% | 6.80% | 0.65% | 0.40% | NA |
| All Japonica | 1512 | 5.40% | 79.00% | 0.13% | 15.48% | NA |
| Aus | 269 | 5.60% | 87.00% | 7.43% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 91.40% | 6.00% | 1.08% | 1.51% | NA |
| Indica III | 913 | 97.50% | 1.80% | 0.44% | 0.33% | NA |
| Indica Intermediate | 786 | 81.30% | 17.40% | 1.15% | 0.13% | NA |
| Temperate Japonica | 767 | 1.20% | 96.00% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 12.10% | 66.50% | 0.40% | 21.03% | NA |
| Japonica Intermediate | 241 | 4.60% | 51.50% | 0.00% | 43.98% | NA |
| VI/Aromatic | 96 | 21.90% | 77.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 54.40% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0707566881 | T -> DEL | LOC_Os07g13190.1 | N | frameshift_variant | Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |
| vg0707566881 | T -> C | LOC_Os07g13190.1 | synonymous_variant ; p.Asn662Asn; LOW | synonymous_codon | Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 60.705 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0707566881 | NA | 5.22E-06 | mr1062 | 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 |
| vg0707566881 | 2.44E-06 | 2.44E-06 | mr1360 | 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 |
| vg0707566881 | 1.27E-06 | 1.18E-06 | mr1525 | 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 |
| vg0707566881 | NA | 9.20E-06 | mr1541 | 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 |
| vg0707566881 | NA | 4.51E-06 | mr1676 | 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 |
| vg0707566881 | NA | 6.54E-06 | mr1968 | 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 |