Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-128_S34_L005_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 24557803
Paired-end alignments with a unique best hit 11023912
Pairs without alignments under any condition 11430018
Pairs that did not map uniquely 2103873
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 342815591
Methylated C's in CpG context 12084385
Methylated C's in CHG context 1712206
Methylated C's in CHH context 2665031
Methylated C's in Unknown context 47752
Unmethylated C's in CpG context 36262181
Unmethylated C's in CHG context 69681804
Unmethylated C's in CHH context 220409984
Unmethylated C's in Unknown context 723863
Percentage methylation (CpG context) 25.0%
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 5468345 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5555565 original bottom strand

Deduplication

Alignments analysed 11023910
Unique alignments 9300124
Duplicates removed 1723786
Duplicated alignments were found at 865786 different positions

Cytosine Methylation after Extraction

Total C's analysed 215109906
Methylated C's in CpG context 8244675
Methylated C's in CHG context 1071477
Methylated C's in CHH context 1772832
Unmethylated C's in CpG context 21307910
Unmethylated C's in CHG context 42824701
Unmethylated C's in CHH context 139888311
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.3%

M-Bias Plot