Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-184_S18_L003_R2_001_val_2.fq.gz

Data processed at 08:15 on 2019-08-08


Alignment Stats

Sequence pairs analysed in total 20689148
Paired-end alignments with a unique best hit 8444730
Pairs without alignments under any condition 10305796
Pairs that did not map uniquely 1938622
Genomic sequence context not extractable (edges of chromosomes) 2

Cytosine Methylation

Total C's analysed 251839676
Methylated C's in CpG context 9669457
Methylated C's in CHG context 1217679
Methylated C's in CHH context 3983200
Methylated C's in Unknown context 60694
Unmethylated C's in CpG context 25706227
Unmethylated C's in CHG context 53487968
Unmethylated C's in CHH context 157775145
Unmethylated C's in Unknown context 557312
Percentage methylation (CpG context) 27.3%
Percentage methylation (CHG context) 2.2%
Percentage methylation (CHH context) 2.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4167553 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4277175 original bottom strand

Deduplication

Alignments analysed 8444728
Unique alignments 6296462
Duplicates removed 2148266
Duplicated alignments were found at 1332291 different positions

Cytosine Methylation after Extraction

Total C's analysed 128398540
Methylated C's in CpG context 5213255
Methylated C's in CHG context 627120
Methylated C's in CHH context 2204316
Unmethylated C's in CpG context 12567730
Unmethylated C's in CHG context 26364706
Unmethylated C's in CHH context 81421413
Percentage methylation (CpG context) 29.3%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.6%

M-Bias Plot