Table 3. Sequencing quality of variants found in the grade III ependymoma.
| Genes | Coding | Allele Coverage | Allele Ratio | p-value | FATHMM
predication |
Phred
Score |
Coverage
(x) |
|---|---|---|---|---|---|---|---|
| IDH1 | c.395G>A | CG=1900, TG=96 | CG=0.9519, TG=0.0481 | 0.00001 | Pathogenic | 221.064 | 1996 |
| ERBB4 | c.421+58A>G | C=1988 | C=1.0 | 0.00001 | NA | 31774.6 | 1988 |
| PIK3CA | c.352+40A>G | A=1038, G=957 | A=0.5203, G=0.4797 | 0.00001 | NA | 9501.82 | 1995 |
| PIK3CA | c.1173A>G | A=915, G=1085 | A=0.4575, G=0.5425 | 0.00001 | Benign | 11555.8 | 2000 |
| FGFR3 | c.1953G>A | A=1993 | A=1.0 | 0.00001 | Benign | 31840.6 | 1993 |
| PDGFRA | c.1701A>G | AGCCCGGATGGACATG=1941 | AGCCCGGATGGACATG=1.0 | 0.00001 | Benign | 35066.6 | 1941 |
| KDR | c.2615-36A>CA | T=1124, TG=864 | T=0.5654, TG=0.4346 | 0.00001 | NA | 5173.27 | 1988 |
| KDR | c.1416A>T | T=971, A=1025 | T=0.4865, A=0.5135 | 0.00001 | Benign | 10583.1 | 1996 |
| KDR | c.798+54G>A | C=33, T=1965 | C=0.0165, T=0.9835 | 0.00001 | NA | 30286.5 | 1998 |
| APC | c.4479G>A | CAG=1985, | CAG=1.0 | 0.00001 | Benign | 35885.9 | 1985 |
| CSF1R,
HMGXB3 |
c.*1841TG>GA,
c.2954_ 2955delCAinsTC |
GA=1977 | GA=1.0 | 0.00001 | Benign | 31540.7 | 1977 |
| EGFR,
EGFR-AS1 |
c.2361G>A | G=579, A=1420 | G=0.2896, A=0.7104 | 0.00001 | Benign | 17657.6 | 1999 |
| RET | c.2307G>T | T=1996 | T=1.0 | 0.00001 | Benign | 31993.7 | 1996 |
| HRAS | c.81T>C | A=1018, G=981 | A=0.5093, G=0.4907 | 0.00001 | Benign | 11998.4 | 1999 |
| FLT3 | c.1776T>C | A=929, G=1069 | A=0.465, G=0.535 | 0.00001 | NA | 11295.9 | 1998 |
| FLT3 | c.1310-3T>C | G=1998 | G=1.0 | 0.00001 | Benign | 32026.3 | 1998 |
| TP53 | c.215C>G | G=1038, C=956 | G=0.5206, C=0.4794 | 0.00001 | Benign | 11559.2 | 1994 |
| SMAD4 | c.1086T>C | T=727, C=1272 | T=0.3637, C=0.6363 | 0.00001 | Benign | 14836.6 | 1999 |
| DERL3,
SMARCB1 |
c.1119-41G>A,
c.*727C>T |
G=950, A=1050 | G=0.475, A=0.525 | 0.00001 | NA | 13246.6 | 2000 |