Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-41_S38_L005_R2_001_val_2.fq.gz

Data processed at 23:49 on 2020-03-24


Alignment Stats

Sequence pairs analysed in total 25055317
Paired-end alignments with a unique best hit 10110534
Pairs without alignments under any condition 12402840
Pairs that did not map uniquely 2541943
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 290510503
Methylated C's in CpG context 12940226
Methylated C's in CHG context 1543391
Methylated C's in CHH context 4910085
Methylated C's in Unknown context 96039
Unmethylated C's in CpG context 28119492
Unmethylated C's in CHG context 60698341
Unmethylated C's in CHH context 182298968
Unmethylated C's in Unknown context 604385
Percentage methylation (CpG context) 31.5%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4993663 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5116869 original bottom strand

Deduplication

Alignments analysed 10110532
Unique alignments 6399320
Duplicates removed 3711212
Duplicated alignments were found at 2206337 different positions

Cytosine Methylation after Extraction

Total C's analysed 128539262
Methylated C's in CpG context 5867583
Methylated C's in CHG context 687621
Methylated C's in CHH context 2454676
Unmethylated C's in CpG context 11862497
Unmethylated C's in CHG context 26124666
Unmethylated C's in CHH context 81542219
Percentage methylation (CpG context) 33.1%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.9%

M-Bias Plot