Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-220_S32_L004_R2_001_val_2.fq.gz

Data processed at 12:47 on 2019-08-08


Alignment Stats

Sequence pairs analysed in total 15670592
Paired-end alignments with a unique best hit 6443741
Pairs without alignments under any condition 7744109
Pairs that did not map uniquely 1482742
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 192776371
Methylated C's in CpG context 7792143
Methylated C's in CHG context 1027385
Methylated C's in CHH context 3406922
Methylated C's in Unknown context 57729
Unmethylated C's in CpG context 19534468
Unmethylated C's in CHG context 40565305
Unmethylated C's in CHH context 120450148
Unmethylated C's in Unknown context 422486
Percentage methylation (CpG context) 28.5%
Percentage methylation (CHG context) 2.5%
Percentage methylation (CHH context) 2.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3171588 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 3272152 original bottom strand

Deduplication

Alignments analysed 6443740
Unique alignments 4362357
Duplicates removed 2081383
Duplicated alignments were found at 1265421 different positions

Cytosine Methylation after Extraction

Total C's analysed 89710026
Methylated C's in CpG context 3860035
Methylated C's in CHG context 483168
Methylated C's in CHH context 1807632
Unmethylated C's in CpG context 8426280
Unmethylated C's in CHG context 18264364
Unmethylated C's in CHH context 56868547
Percentage methylation (CpG context) 31.4%
Percentage methylation (CHG context) 2.6%
Percentage methylation (CHH context) 3.1%

M-Bias Plot