Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-113_S30_L005_R2_001_val_2.fq.gz

Data processed at 20:04 on 2019-08-12


Alignment Stats

Sequence pairs analysed in total 26302191
Paired-end alignments with a unique best hit 11581686
Pairs without alignments under any condition 12489960
Pairs that did not map uniquely 2230545
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 359357698
Methylated C's in CpG context 12471829
Methylated C's in CHG context 1771590
Methylated C's in CHH context 2827755
Methylated C's in Unknown context 53715
Unmethylated C's in CpG context 37593518
Unmethylated C's in CHG context 73195958
Unmethylated C's in CHH context 231497048
Unmethylated C's in Unknown context 768555
Percentage methylation (CpG context) 24.9%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5744513 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5837172 original bottom strand

Deduplication

Alignments analysed 11581685
Unique alignments 9854743
Duplicates removed 1726942
Duplicated alignments were found at 879906 different positions

Cytosine Methylation after Extraction

Total C's analysed 224084049
Methylated C's in CpG context 8423482
Methylated C's in CHG context 1104529
Methylated C's in CHH context 1867274
Unmethylated C's in CpG context 22028913
Unmethylated C's in CHG context 44713152
Unmethylated C's in CHH context 145946699
Percentage methylation (CpG context) 27.7%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.3%

M-Bias Plot