Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-127_S33_L005_R2_001_val_2.fq.gz

Data processed at 05:39 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 22262118
Paired-end alignments with a unique best hit 9986595
Pairs without alignments under any condition 10417464
Pairs that did not map uniquely 1858059
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 314010295
Methylated C's in CpG context 11042968
Methylated C's in CHG context 1520028
Methylated C's in CHH context 2541364
Methylated C's in Unknown context 47519
Unmethylated C's in CpG context 33055152
Unmethylated C's in CHG context 64128787
Unmethylated C's in CHH context 201721996
Unmethylated C's in Unknown context 647317
Percentage methylation (CpG context) 25.0%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 1.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4954421 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5032173 original bottom strand

Deduplication

Alignments analysed 9986594
Unique alignments 8450079
Duplicates removed 1536515
Duplicated alignments were found at 782021 different positions

Cytosine Methylation after Extraction

Total C's analysed 196938082
Methylated C's in CpG context 7564205
Methylated C's in CHG context 967557
Methylated C's in CHH context 1694338
Unmethylated C's in CpG context 19544907
Unmethylated C's in CHG context 39233900
Unmethylated C's in CHH context 127933175
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.3%

M-Bias Plot