Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-151_S2_L002_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 24505793
Paired-end alignments with a unique best hit 9915442
Pairs without alignments under any condition 12555282
Pairs that did not map uniquely 2035069
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 303264962
Methylated C's in CpG context 12323211
Methylated C's in CHG context 1414630
Methylated C's in CHH context 3533701
Methylated C's in Unknown context 52135
Unmethylated C's in CpG context 31194293
Unmethylated C's in CHG context 65160946
Unmethylated C's in CHH context 189638181
Unmethylated C's in Unknown context 646387
Percentage methylation (CpG context) 28.3%
Percentage methylation (CHG context) 2.1%
Percentage methylation (CHH context) 1.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4881878 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5033563 original bottom strand

Deduplication

Alignments analysed 9915441
Unique alignments 7210277
Duplicates removed 2705164
Duplicated alignments were found at 1698251 different positions

Cytosine Methylation after Extraction

Total C's analysed 154371720
Methylated C's in CpG context 6619617
Methylated C's in CHG context 739999
Methylated C's in CHH context 1943298
Unmethylated C's in CpG context 14863708
Unmethylated C's in CHG context 32156644
Unmethylated C's in CHH context 98048454
Percentage methylation (CpG context) 30.8%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 1.9%

M-Bias Plot