| Variant ID: vg1007738391 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7738391 |
| Reference Allele: G | Alternative Allele: C,T |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, G: 0.19, others allele: 0.00, population size: 218. )
CAAACTACCAGGTGCCACCAGATGACTGTCCAGTACCACCAGTGCGTATAAATTCCAAGCGCCTAGCGGCGTCCTTGAGTCGAACAAAGCATTTGCAGGT[G/C,T]
AATGGGTCACGGAATAGCGCACAAGCAGCATACCACACACTTCCTCCAATTTCATGGCCATCATTTTCCACCAACTCCATGCACGCATCAAGGCCCATAG
CTATGGGCCTTGATGCGTGCATGGAGTTGGTGGAAAATGATGGCCATGAAATTGGAGGAAGTGTGTGGTATGCTGCTTGTGCGCTATTCCGTGACCCATT[C/G,A]
ACCTGCAAATGCTTTGTTCGACTCAAGGACGCCGCTAGGCGCTTGGAATTTATACGCACTGGTGGTACTGGACAGTCATCTGGTGGCACCTGGTAGTTTG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.90% | 1.80% | 39.23% | 29.09% | T: 0.04% |
| All Indica | 2759 | 28.00% | 0.30% | 42.15% | 29.50% | NA |
| All Japonica | 1512 | 39.50% | 5.00% | 24.47% | 31.02% | T: 0.07% |
| Aus | 269 | 1.90% | 0.00% | 84.01% | 14.13% | NA |
| Indica I | 595 | 42.40% | 0.20% | 24.87% | 32.61% | NA |
| Indica II | 465 | 12.30% | 0.00% | 48.82% | 38.92% | NA |
| Indica III | 913 | 26.10% | 0.00% | 51.48% | 22.45% | NA |
| Indica Intermediate | 786 | 28.80% | 1.00% | 40.46% | 29.77% | NA |
| Temperate Japonica | 767 | 53.70% | 9.80% | 16.30% | 20.21% | NA |
| Tropical Japonica | 504 | 10.30% | 0.00% | 43.85% | 45.83% | NA |
| Japonica Intermediate | 241 | 55.20% | 0.00% | 9.96% | 34.44% | T: 0.41% |
| VI/Aromatic | 96 | 3.10% | 0.00% | 64.58% | 32.29% | NA |
| Intermediate | 90 | 36.70% | 0.00% | 36.67% | 25.56% | T: 1.11% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007738391 | G -> C | LOC_Os10g14290.1 | missense_variant ; p.Phe373Leu; MODERATE | nonsynonymous_codon ; F373L | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | unknown | unknown | TOLERATED | 0.29 |
| vg1007738391 | G -> T | LOC_Os10g14290.1 | missense_variant ; p.Phe373Leu; MODERATE | nonsynonymous_codon ; F373L | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | unknown | unknown | TOLERATED | 0.29 |
| vg1007738391 | G -> DEL | LOC_Os10g14290.1 | N | frameshift_variant | Average:6.018; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |