Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-167_S10_L002_R2_001_val_2.fq.gz

Data processed at 11:37 on 2019-08-07


Alignment Stats

Sequence pairs analysed in total 24481250
Paired-end alignments with a unique best hit 10438000
Pairs without alignments under any condition 12046563
Pairs that did not map uniquely 1996687
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 327276929
Methylated C's in CpG context 12357096
Methylated C's in CHG context 2047643
Methylated C's in CHH context 6308688
Methylated C's in Unknown context 65277
Unmethylated C's in CpG context 31908920
Unmethylated C's in CHG context 67977563
Unmethylated C's in CHH context 206677019
Unmethylated C's in Unknown context 705078
Percentage methylation (CpG context) 27.9%
Percentage methylation (CHG context) 2.9%
Percentage methylation (CHH context) 3.0%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 5166645 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 5271355 original bottom strand

Deduplication

Alignments analysed 10438000
Unique alignments 7635088
Duplicates removed 2802912
Duplicated alignments were found at 1823622 different positions

Cytosine Methylation after Extraction

Total C's analysed 169475057
Methylated C's in CpG context 6721143
Methylated C's in CHG context 1081552
Methylated C's in CHH context 3482873
Unmethylated C's in CpG context 15986854
Unmethylated C's in CHG context 34252524
Unmethylated C's in CHH context 107950111
Percentage methylation (CpG context) 29.6%
Percentage methylation (CHG context) 3.1%
Percentage methylation (CHH context) 3.1%

M-Bias Plot