Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-43_S40_L005_R2_001_val_2.fq.gz

Data processed at 20:04 on 2019-08-12


Alignment Stats

Sequence pairs analysed in total 22573555
Paired-end alignments with a unique best hit 10112774
Pairs without alignments under any condition 10003930
Pairs that did not map uniquely 2456851
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 291124282
Methylated C's in CpG context 12587981
Methylated C's in CHG context 1494744
Methylated C's in CHH context 5077384
Methylated C's in Unknown context 67963
Unmethylated C's in CpG context 28303550
Unmethylated C's in CHG context 60291324
Unmethylated C's in CHH context 183369299
Unmethylated C's in Unknown context 592883
Percentage methylation (CpG context) 30.8%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5003413 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5109361 original bottom strand

Deduplication

Alignments analysed 10112774
Unique alignments 6420611
Duplicates removed 3692163
Duplicated alignments were found at 2223544 different positions

Cytosine Methylation after Extraction

Total C's analysed 128026299
Methylated C's in CpG context 5689722
Methylated C's in CHG context 671794
Methylated C's in CHH context 2537937
Unmethylated C's in CpG context 11970270
Unmethylated C's in CHG context 25906277
Unmethylated C's in CHH context 81250299
Percentage methylation (CpG context) 32.2%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 3.0%

M-Bias Plot