| Variant ID: vg0900561007 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 561007 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAGGAGAGCAGATTACTCGGCATTTCATCAAGTGCCGATTGGCACCAATTAAAGAAAGATCCCGTACAGCATTCGAGTTCGACGGCAAACATGATCCCAA[T/C]
CGTGAAGAACCAGACTCTCTGGACTTTAAAATCATGAAGGAGAGAATGTATAAAATTTTCTCAAATGCTATTGTCGTTAGCTACTCACATCAGCTGCCAG
CTGGCAGCTGATGTGAGTAGCTAACGACAATAGCATTTGAGAAAATTTTATACATTCTCTCCTTCATGATTTTAAAGTCCAGAGAGTCTGGTTCTTCACG[A/G]
TTGGGATCATGTTTGCCGTCGAACTCGAATGCTGTACGGGATCTTTCTTTAATTGGTGCCAATCGGCACTTGATGAAATGCCGAGTAATCTGCTCTCCTT
| 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 | 32.00% | 5.20% | 22.66% | 40.18% | NA |
| All Indica | 2759 | 7.20% | 2.40% | 30.30% | 60.09% | NA |
| All Japonica | 1512 | 80.80% | 0.20% | 6.48% | 12.57% | NA |
| Aus | 269 | 3.30% | 62.10% | 34.20% | 0.37% | NA |
| Indica I | 595 | 6.70% | 0.70% | 21.85% | 70.76% | NA |
| Indica II | 465 | 3.40% | 1.90% | 31.40% | 63.23% | NA |
| Indica III | 913 | 9.50% | 3.60% | 34.06% | 52.79% | NA |
| Indica Intermediate | 786 | 7.30% | 2.40% | 31.68% | 58.65% | NA |
| Temperate Japonica | 767 | 71.40% | 0.10% | 10.43% | 17.99% | NA |
| Tropical Japonica | 504 | 97.00% | 0.40% | 0.99% | 1.59% | NA |
| Japonica Intermediate | 241 | 76.30% | 0.00% | 5.39% | 18.26% | NA |
| VI/Aromatic | 96 | 34.40% | 6.20% | 36.46% | 22.92% | NA |
| Intermediate | 90 | 54.40% | 3.30% | 11.11% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0900561007 | T -> DEL | LOC_Os09g01810.1 | N | frameshift_variant | Average:19.935; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| vg0900561007 | T -> C | LOC_Os09g01810.1 | synonymous_variant ; p.Asn250Asn; LOW | synonymous_codon | Average:19.935; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0900561007 | NA | 2.70E-06 | mr1100_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 |
| vg0900561007 | NA | 1.32E-08 | mr1402_2 | 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 |
| vg0900561007 | NA | 3.61E-06 | mr1613_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 |
| vg0900561007 | NA | 1.01E-06 | mr1619_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 |
| vg0900561007 | NA | 3.34E-08 | mr1795_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 |
| vg0900561007 | NA | 1.30E-06 | mr1913_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 |
| vg0900561007 | NA | 2.48E-08 | mr1962_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 |