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 05:18 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 21488138
Paired-end alignments with a unique best hit 8423411
Pairs without alignments under any condition 10776872
Pairs that did not map uniquely 2287855
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 235029500
Methylated C's in CpG context 8853859
Methylated C's in CHG context 1292583
Methylated C's in CHH context 3088082
Methylated C's in Unknown context 52541
Unmethylated C's in CpG context 25257864
Unmethylated C's in CHG context 49422337
Unmethylated C's in CHH context 147114775
Unmethylated C's in Unknown context 499727
Percentage methylation (CpG context) 26.0%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.1%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4160590 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4262820 original bottom strand

Deduplication

Alignments analysed 8423410
Unique alignments 6192833
Duplicates removed 2230577
Duplicated alignments were found at 1361870 different positions

Cytosine Methylation after Extraction

Total C's analysed 115906900
Methylated C's in CpG context 4644294
Methylated C's in CHG context 619856
Methylated C's in CHH context 1638581
Unmethylated C's in CpG context 11620008
Unmethylated C's in CHG context 23551619
Unmethylated C's in CHH context 73832542
Percentage methylation (CpG context) 28.6%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 2.2%

M-Bias Plot