Bismark alignment report total C base number problem.

Question

[MatthewP]

Hello, I want to calculate BS treatment convert rate. After bismark command map reads to _Enterobacteria phage lambda_ genome the bismark mapping report is confusing.

Final Cytosine Methylation Report
=================================
Total number of C's analysed:   109353193

Total methylated C's in CpG context:    92584
Total methylated C's in CHG context:    117087
Total methylated C's in CHH context:    267258
Total methylated C's in Unknown context:        120

Total unmethylated C's in CpG context:  25329922
Total unmethylated C's in CHG context:  26636644
Total unmethylated C's in CHH context:  56909698
Total unmethylated C's in Unknown context:      9569

C methylated in CpG context:    0.4%
C methylated in CHG context:    0.4%
C methylated in CHH context:    0.5%
C methylated in unknown context (CN or CHN):    1.2%


Bismark completed in 0d 9h 0m 24s

Here total number of C base: 109353193
Total number of methylated C: 92584 + 117087 + 267258 + 120 = 477049
Total number of unmethylated C: 25329922 + 26636644 + 56909698 + 9569 = 108885833
But when I plus methylated and unmethylated C, the number don't equal to total number of C reported: 477049 + 108885833 = 109362882 != 109353193

What's wrong here?

Answer 1

[MatthewP]

Mayby there is some overlap C, remove unknown context data will fix this problem.

> 92584 + 117087 + 267258 + 25329922 + 26636644 + 56909698
[1] 109353193