Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-188_S21_L003_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 40447
Pairs without alignments under any condition 47066
Pairs that did not map uniquely 12487
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 1138212
Methylated C's in CpG context 41493
Methylated C's in CHG context 6520
Methylated C's in CHH context 42401
Methylated C's in Unknown context 699
Unmethylated C's in CpG context 117465
Unmethylated C's in CHG context 229470
Unmethylated C's in CHH context 700863
Unmethylated C's in Unknown context 2554
Percentage methylation (CpG context) 26.1%
Percentage methylation (CHG context) 2.8%
Percentage methylation (CHH context) 5.7%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 18875 original top strand
CTOT 1293 complementary to original top strand
CTOB 1266 complementary to original bottom strand
OB 19013 original bottom strand

Cytosine Methylation after Extraction

Total C's analysed 758107
Methylated C's in CpG context 27915
Methylated C's in CHG context 4248
Methylated C's in CHH context 25738
Unmethylated C's in CpG context 77391
Unmethylated C's in CHG context 152113
Unmethylated C's in CHH context 470702
Percentage methylation (CpG context) 26.5%
Percentage methylation (CHG context) 2.7%
Percentage methylation (CHH context) 5.2%

M-Bias Plot