Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-199_S24_L003_R2_001_val_2.fq.gz

Data processed at 18:21 on 2019-07-02


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 41233
Pairs without alignments under any condition 47638
Pairs that did not map uniquely 11129
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1207297
Methylated C's in CpG context 51102
Methylated C's in CHG context 6936
Methylated C's in CHH context 57304
Methylated C's in Unknown context 889
Unmethylated C's in CpG context 114819
Unmethylated C's in CHG context 244162
Unmethylated C's in CHH context 732974
Unmethylated C's in Unknown context 2878
Percentage methylation (CpG context) 30.8%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 7.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 18668 original top strand
CTOT 1445 complementary to original top strand
CTOB 1531 complementary to original bottom strand
OB 19589 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 834824
Methylated C's in CpG context 35595
Methylated C's in CHG context 4728
Methylated C's in CHH context 36683
Unmethylated C's in CpG context 79123
Unmethylated C's in CHG context 168056
Unmethylated C's in CHH context 510639
Percentage methylation (CpG context) 31.0%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 6.7%

M-Bias Plot