Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-104_S28_L005_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 46064
Pairs without alignments under any condition 44273
Pairs that did not map uniquely 9663
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1432969
Methylated C's in CpG context 51586
Methylated C's in CHG context 7144
Methylated C's in CHH context 42020
Methylated C's in Unknown context 485
Unmethylated C's in CpG context 136387
Unmethylated C's in CHG context 284339
Unmethylated C's in CHH context 911493
Unmethylated C's in Unknown context 3198
Percentage methylation (CpG context) 27.4%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 4.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 22319 original top strand
CTOT 621 complementary to original top strand
CTOB 654 complementary to original bottom strand
OB 22470 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 1032571
Methylated C's in CpG context 38014
Methylated C's in CHG context 5157
Methylated C's in CHH context 27407
Unmethylated C's in CpG context 98076
Unmethylated C's in CHG context 204141
Unmethylated C's in CHH context 659776
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 4.0%

M-Bias Plot