Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-162_S9_L002_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 22769546
Paired-end alignments with a unique best hit 8267039
Pairs without alignments under any condition 12467371
Pairs that did not map uniquely 2035136
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 238005650
Methylated C's in CpG context 8810888
Methylated C's in CHG context 1190010
Methylated C's in CHH context 3285737
Methylated C's in Unknown context 56519
Unmethylated C's in CpG context 24654378
Unmethylated C's in CHG context 50555362
Unmethylated C's in CHH context 149509275
Unmethylated C's in Unknown context 528637
Percentage methylation (CpG context) 26.3%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4073674 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4193365 original bottom strand

Deduplication

Alignments analysed 8267039
Unique alignments 6383164
Duplicates removed 1883875
Duplicated alignments were found at 1160963 different positions

Cytosine Methylation after Extraction

Total C's analysed 122908719
Methylated C's in CpG context 4824979
Methylated C's in CHG context 612515
Methylated C's in CHH context 1827593
Unmethylated C's in CpG context 12090566
Unmethylated C's in CHG context 25238601
Unmethylated C's in CHH context 78314465
Percentage methylation (CpG context) 28.5%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.3%

M-Bias Plot