Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-135_S35_L005_R2_001_val_2.fq.gz

Data processed at 05:39 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 28731808
Paired-end alignments with a unique best hit 12720631
Pairs without alignments under any condition 13210078
Pairs that did not map uniquely 2801099
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 379885177
Methylated C's in CpG context 14174074
Methylated C's in CHG context 2097825
Methylated C's in CHH context 3204273
Methylated C's in Unknown context 64166
Unmethylated C's in CpG context 39497431
Unmethylated C's in CHG context 77915331
Unmethylated C's in CHH context 242996243
Unmethylated C's in Unknown context 785379
Percentage methylation (CpG context) 26.4%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 1.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 6307893 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6412737 original bottom strand

Deduplication

Alignments analysed 12720630
Unique alignments 10559504
Duplicates removed 2161126
Duplicated alignments were found at 1085821 different positions

Cytosine Methylation after Extraction

Total C's analysed 225992948
Methylated C's in CpG context 9046557
Methylated C's in CHG context 1202237
Methylated C's in CHH context 2001278
Unmethylated C's in CpG context 21842118
Unmethylated C's in CHG context 45361388
Unmethylated C's in CHH context 146539370
Percentage methylation (CpG context) 29.3%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 1.3%

M-Bias Plot