Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_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 41120
Pairs without alignments under any condition 47679
Pairs that did not map uniquely 11201
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1210712
Methylated C's in CpG context 45834
Methylated C's in CHG context 6782
Methylated C's in CHH context 54452
Methylated C's in Unknown context 731
Unmethylated C's in CpG context 121772
Unmethylated C's in CHG context 247802
Unmethylated C's in CHH context 734070
Unmethylated C's in Unknown context 2695
Percentage methylation (CpG context) 27.3%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 6.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 18966 original top strand
CTOT 1212 complementary to original top strand
CTOB 1265 complementary to original bottom strand
OB 19677 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 818462
Methylated C's in CpG context 31357
Methylated C's in CHG context 4529
Methylated C's in CHH context 34479
Unmethylated C's in CpG context 81829
Unmethylated C's in CHG context 166275
Unmethylated C's in CHH context 499993
Percentage methylation (CpG context) 27.7%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 6.5%

M-Bias Plot