| Variant ID: vg0727574396 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27574396 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTTCTTGAACTGTAGGGGTTCTAGGAATGATATTTCCTAGTTCATTATATTTATGCTTATTTGGTGAACTTTCTGTAGTTCTCCCTTGGGCTGATAAGT[C/T]
TCTTTTAGGTGCCATAGCCCTGTAAAAATTCACGAGATAAGAAATCTGGTAGGGAGTTTAATTCTCCCTTGATATATTCTATTTCAAAGTCAAAGCATGA
TCATGCTTTGACTTTGAAATAGAATATATCAAGGGAGAATTAAACTCCCTACCAGATTTCTTATCTCGTGAATTTTTACAGGGCTATGGCACCTAAAAGA[G/A]
ACTTATCAGCCCAAGGGAGAACTACAGAAAGTTCACCAAATAAGCATAAATATAATGAACTAGGAAATATCATTCCTAGAACCCCTACAGTTCAAGAAAA
| 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 | 73.70% | 9.80% | 10.28% | 6.28% | NA |
| All Indica | 2759 | 83.50% | 0.50% | 6.78% | 9.17% | NA |
| All Japonica | 1512 | 56.00% | 29.10% | 13.03% | 1.85% | NA |
| Aus | 269 | 88.80% | 0.40% | 6.69% | 4.09% | NA |
| Indica I | 595 | 88.90% | 0.30% | 5.04% | 5.71% | NA |
| Indica II | 465 | 90.10% | 0.00% | 5.16% | 4.73% | NA |
| Indica III | 913 | 76.60% | 0.10% | 8.98% | 14.35% | NA |
| Indica Intermediate | 786 | 83.70% | 1.40% | 6.49% | 8.40% | NA |
| Temperate Japonica | 767 | 72.40% | 11.70% | 13.82% | 2.09% | NA |
| Tropical Japonica | 504 | 36.70% | 49.40% | 12.50% | 1.39% | NA |
| Japonica Intermediate | 241 | 44.40% | 41.90% | 11.62% | 2.07% | NA |
| VI/Aromatic | 96 | 25.00% | 4.20% | 69.79% | 1.04% | NA |
| Intermediate | 90 | 74.40% | 2.20% | 18.89% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0727574396 | C -> DEL | LOC_Os07g46200.1 | N | frameshift_variant | Average:5.411; most accessible tissue: Zhenshan97 young leaf, score: 8.295 | N | N | N | N |
| vg0727574396 | C -> T | LOC_Os07g46200.1 | missense_variant ; p.Asp6Asn; MODERATE | nonsynonymous_codon ; D6N | Average:5.411; most accessible tissue: Zhenshan97 young leaf, score: 8.295 | unknown | unknown | DELETERIOUS | 0.03 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0727574396 | 2.79E-06 | 2.99E-07 | mr1002 | 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 |
| vg0727574396 | NA | 1.36E-12 | mr1002 | 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 |
| vg0727574396 | 6.24E-08 | 1.12E-09 | mr1002_2 | 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 |
| vg0727574396 | NA | 5.54E-14 | mr1002_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 |