Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-136_S36_L005_R2_001_val_2.fq.gz

Data processed at 02:53 on 2020-01-03


Alignment Stats

Sequence pairs analysed in total 27792315
Paired-end alignments with a unique best hit 12229034
Pairs without alignments under any condition 12912342
Pairs that did not map uniquely 2650939
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 371098859
Methylated C's in CpG context 12526554
Methylated C's in CHG context 1883224
Methylated C's in CHH context 2923602
Methylated C's in Unknown context 54090
Unmethylated C's in CpG context 39735089
Unmethylated C's in CHG context 76137777
Unmethylated C's in CHH context 237892613
Unmethylated C's in Unknown context 810936
Percentage methylation (CpG context) 24.0%
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 6066303 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 6162730 original bottom strand

Deduplication

Alignments analysed 12229033
Unique alignments 10289878
Duplicates removed 1939155
Duplicated alignments were found at 929619 different positions

Cytosine Methylation after Extraction

Total C's analysed 222520026
Methylated C's in CpG context 8205504
Methylated C's in CHG context 1105916
Methylated C's in CHH context 1849444
Unmethylated C's in CpG context 22514794
Unmethylated C's in CHG context 44690621
Unmethylated C's in CHH context 144153747
Percentage methylation (CpG context) 26.7%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 1.3%

M-Bias Plot