| Variant ID: vg0711997472 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 11997472 |
| Reference Allele: G | Alternative Allele: C,A |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGATTCGGCGGCCGTTTCTTTTTATCATCTTGTTCATCCATGATGTGAGCAACGGTTGTATCTGTAGTAGCCGTGGTCACATCATCCTCCCCTTCTTCAT[G/C,A]
GAAAACCGTCCTCGGTTTTTCCAAATGGTGCTCATGGCATGGTCTGTTTAAAATAACCTGTTTCATCCAATAAAAACAAGAGAAACTCGAAGTAATATGA
TCATATTACTTCGAGTTTCTCTTGTTTTTATTGGATGAAACAGGTTATTTTAAACAGACCATGCCATGAGCACCATTTGGAAAAACCGAGGACGGTTTTC[C/G,T]
ATGAAGAAGGGGAGGATGATGTGACCACGGCTACTACAGATACAACCGTTGCTCACATCATGGATGAACAAGATGATAAAAAGAAACGGCCGCCGAATCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.20% | 19.00% | 0.30% | 20.38% | A: 0.15% |
| All Indica | 2759 | 93.00% | 2.60% | 0.07% | 4.13% | A: 0.14% |
| All Japonica | 1512 | 3.60% | 47.20% | 0.13% | 49.01% | NA |
| Aus | 269 | 58.70% | 6.30% | 3.72% | 30.11% | A: 1.12% |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.30% | 1.90% | 0.00% | 4.30% | A: 0.43% |
| Indica III | 913 | 94.30% | 0.20% | 0.11% | 5.26% | A: 0.11% |
| Indica Intermediate | 786 | 86.00% | 7.90% | 0.13% | 5.85% | A: 0.13% |
| Temperate Japonica | 767 | 3.30% | 74.20% | 0.13% | 22.43% | NA |
| Tropical Japonica | 504 | 3.20% | 12.10% | 0.20% | 84.52% | NA |
| Japonica Intermediate | 241 | 5.80% | 34.90% | 0.00% | 59.34% | NA |
| VI/Aromatic | 96 | 17.70% | 76.00% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 54.40% | 22.20% | 0.00% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0711997472 | G -> DEL | N | N | silent_mutation | Average:39.825; most accessible tissue: Zhenshan97 young leaf, score: 55.899 | N | N | N | N |
| vg0711997472 | G -> A | LOC_Os07g20730.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.825; most accessible tissue: Zhenshan97 young leaf, score: 55.899 | N | N | N | N |
| vg0711997472 | G -> C | LOC_Os07g20730.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.825; most accessible tissue: Zhenshan97 young leaf, score: 55.899 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0711997472 | 2.30E-06 | NA | mr1802 | 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 |
| vg0711997472 | 5.04E-06 | 5.03E-06 | mr1802 | 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 |
| vg0711997472 | NA | 1.89E-06 | mr1977 | 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 |