Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-208_S28_L004_R2_001_val_2.fq.gz

Data processed at 17:55 on 2018-10-25


Alignment Stats

Sequence pairs analysed in total 10000
Paired-end alignments with a unique best hit 5665
Pairs without alignments under any condition 2558
Pairs that did not map uniquely 1777
Genomic sequence context not extractable (edges of chromosomes) 31

Cytosine Methylation

Total C's analysed 165086
Methylated C's in CpG context 4498
Methylated C's in CHG context 985
Methylated C's in CHH context 10010
Methylated C's in Unknown context 507
Unmethylated C's in CpG context 17585
Unmethylated C's in CHG context 33562
Unmethylated C's in CHH context 98446
Unmethylated C's in Unknown context 1127
Percentage methylation (CpG context) 20.4%
Percentage methylation (CHG context) 2.9%
Percentage methylation (CHH context) 9.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2471 original top strand
CTOT 398 complementary to original top strand
CTOB 391 complementary to original bottom strand
OB 2374 original bottom strand

Deduplication

Alignments analysed 5634
Unique alignments 5551
Duplicates removed 83
Duplicated alignments were found at 41 different positions

Cytosine Methylation after Extraction

Total C's analysed 115980
Methylated C's in CpG context 3196
Methylated C's in CHG context 763
Methylated C's in CHH context 8084
Unmethylated C's in CpG context 12076
Unmethylated C's in CHG context 22936
Unmethylated C's in CHH context 68925
Percentage methylation (CpG context) 20.9%
Percentage methylation (CHG context) 3.2%
Percentage methylation (CHH context) 10.5%

M-Bias Plot