Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-230_S37_L004_R2_001_val_2.fq.gz

Data processed at 05:18 on 2019-12-21


Alignment Stats

Sequence pairs analysed in total 29439432
Paired-end alignments with a unique best hit 11206080
Pairs without alignments under any condition 15456327
Pairs that did not map uniquely 2777025
Genomic sequence context not extractable (edges of chromosomes) 3

Cytosine Methylation

Total C's analysed 319285007
Methylated C's in CpG context 13011809
Methylated C's in CHG context 1476854
Methylated C's in CHH context 3593317
Methylated C's in Unknown context 73261
Unmethylated C's in CpG context 33278910
Unmethylated C's in CHG context 67397808
Unmethylated C's in CHH context 200526309
Unmethylated C's in Unknown context 692785
Percentage methylation (CpG context) 28.1%
Percentage methylation (CHG context) 2.1%
Percentage methylation (CHH context) 1.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5519967 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5686110 original bottom strand

Deduplication

Alignments analysed 11206077
Unique alignments 7282444
Duplicates removed 3923633
Duplicated alignments were found at 2312024 different positions

Cytosine Methylation after Extraction

Total C's analysed 139950493
Methylated C's in CpG context 5977998
Methylated C's in CHG context 651184
Methylated C's in CHH context 1768421
Unmethylated C's in CpG context 13704103
Unmethylated C's in CHG context 28593233
Unmethylated C's in CHH context 89255554
Percentage methylation (CpG context) 30.4%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 1.9%

M-Bias Plot