| Variant ID: vg0711196143 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11196143 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTTGACGGCGAACGTGGCAACTCCTTCTTCATCACTTGAGCTTGACTCGGAGTCGGAGCCGAAGATCATCCCAAGATGAGCTTGGCCATAGCAATCATG[T/C]
TTGCTATGCTTGTGCTTCTCCTTCTTCTCAAGCTTCTTCTTGTCTTCCTTGAAGTGGGAGCAATCCTTGATGTGGGGGCAATCCGCAATGAAGTGCCCGG
CCGGGCACTTCATTGCGGATTGCCCCCACATCAAGGATTGCTCCCACTTCAAGGAAGACAAGAAGAAGCTTGAGAAGAAGGAGAAGCACAAGCATAGCAA[A/G]
CATGATTGCTATGGCCAAGCTCATCTTGGGATGATCTTCGGCTCCGACTCCGAGTCAAGCTCAAGTGATGAAGAAGGAGTTGCCACGTTCGCCGTCAAGC
| 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 | 28.70% | 1.30% | 1.14% | 68.81% | NA |
| All Indica | 2759 | 5.50% | 0.60% | 1.67% | 92.21% | NA |
| All Japonica | 1512 | 76.50% | 0.00% | 0.26% | 23.28% | NA |
| Aus | 269 | 2.60% | 16.70% | 1.49% | 79.18% | NA |
| Indica I | 595 | 8.10% | 0.20% | 1.85% | 89.92% | NA |
| Indica II | 465 | 7.70% | 0.00% | 2.58% | 89.68% | NA |
| Indica III | 913 | 2.20% | 1.40% | 0.44% | 95.95% | NA |
| Indica Intermediate | 786 | 6.20% | 0.30% | 2.42% | 91.09% | NA |
| Temperate Japonica | 767 | 69.10% | 0.00% | 0.39% | 30.51% | NA |
| Tropical Japonica | 504 | 86.30% | 0.00% | 0.20% | 13.49% | NA |
| Japonica Intermediate | 241 | 79.30% | 0.00% | 0.00% | 20.75% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 0.00% | 94.79% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 0.00% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0711196143 | T -> DEL | LOC_Os07g18890.1 | N | frameshift_variant | Average:9.399; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0711196143 | T -> C | LOC_Os07g18890.1 | synonymous_variant ; p.Lys310Lys; LOW | synonymous_codon | Average:9.399; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711196143 | 5.66E-06 | 8.34E-06 | mr1094 | 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 |
| vg0711196143 | 1.40E-07 | 1.83E-07 | mr1096 | 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 |
| vg0711196143 | 4.10E-06 | 6.88E-13 | mr1233 | 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 |
| vg0711196143 | NA | 3.35E-24 | mr1548 | 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 |
| vg0711196143 | NA | 5.30E-20 | mr1588 | 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 |
| vg0711196143 | NA | 6.04E-09 | mr1637 | 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 |
| vg0711196143 | 1.13E-07 | 1.13E-07 | mr1973 | 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 |