| Variant ID: vg0102531005 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 2531005 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATATAATAAGATTAATGGTTGTCTCAACCTCACAGTACCGAAGCATTTGAGATCAGGTGGTGATTAGTTCGGCCAGTACGTGAGCTGACTATGATGCAGG[T/C]
CGGTAGAGACAATCTGGAGATGCTGCAGCAGGTCGGTAGCTACAGTCTTGAGATCGGCGCCGCCGAAGCCGCCGGAGTCGCTGGCGAAGAGTACCGCTCC
GGAGCGGTACTCTTCGCCAGCGACTCCGGCGGCTTCGGCGGCGCCGATCTCAAGACTGTAGCTACCGACCTGCTGCAGCATCTCCAGATTGTCTCTACCG[A/G]
CCTGCATCATAGTCAGCTCACGTACTGGCCGAACTAATCACCACCTGATCTCAAATGCTTCGGTACTGTGAGGTTGAGACAACCATTAATCTTATTATAT
| 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 | 48.40% | 5.10% | 17.22% | 29.26% | NA |
| All Indica | 2759 | 29.40% | 5.70% | 24.14% | 40.74% | NA |
| All Japonica | 1512 | 83.30% | 0.80% | 3.64% | 12.30% | NA |
| Aus | 269 | 27.90% | 24.50% | 24.91% | 22.68% | NA |
| Indica I | 595 | 9.20% | 3.70% | 27.90% | 59.16% | NA |
| Indica II | 465 | 32.70% | 4.30% | 20.00% | 43.01% | NA |
| Indica III | 913 | 39.80% | 6.50% | 26.29% | 27.49% | NA |
| Indica Intermediate | 786 | 30.70% | 7.30% | 21.25% | 40.84% | NA |
| Temperate Japonica | 767 | 86.20% | 0.40% | 3.39% | 10.04% | NA |
| Tropical Japonica | 504 | 79.60% | 1.60% | 4.37% | 14.48% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.40% | 2.90% | 14.94% | NA |
| VI/Aromatic | 96 | 80.20% | 4.20% | 14.58% | 1.04% | NA |
| Intermediate | 90 | 72.20% | 2.20% | 13.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0102531005 | T -> DEL | LOC_Os01g05350.1 | N | frameshift_variant | Average:70.322; most accessible tissue: Callus, score: 87.858 | N | N | N | N |
| vg0102531005 | T -> C | LOC_Os01g05350.1 | missense_variant&splice_region_variant ; p.Val95Ala; MODERATE | nonsynonymous_codon ; V95A | Average:70.322; most accessible tissue: Callus, score: 87.858 | unknown | unknown | TOLERATED | 0.40 |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0102531005 | NA | 6.84E-06 | mr1117 | 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 |
| vg0102531005 | 1.94E-06 | 2.93E-07 | mr1119 | 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 |
| vg0102531005 | 9.73E-06 | 1.18E-06 | mr1123 | 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 |
| vg0102531005 | 1.17E-06 | 7.91E-08 | mr1242 | 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 |
| vg0102531005 | NA | 9.43E-06 | mr1247 | 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 |
| vg0102531005 | 1.49E-07 | 1.49E-07 | mr1967 | 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 |
| vg0102531005 | NA | 5.15E-06 | mr1113_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 |