Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-169_S12_L002_R2_001_val_2.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 21392200
Paired-end alignments with a unique best hit 8408059
Pairs without alignments under any condition 10932504
Pairs that did not map uniquely 2051637
Genomic sequence context not extractable (edges of chromosomes) 4

Cytosine Methylation

Total C's analysed 245148711
Methylated C's in CpG context 9715161
Methylated C's in CHG context 1293014
Methylated C's in CHH context 3765782
Methylated C's in Unknown context 64209
Unmethylated C's in CpG context 25600954
Unmethylated C's in CHG context 52728521
Unmethylated C's in CHH context 152045279
Unmethylated C's in Unknown context 533680
Percentage methylation (CpG context) 27.5%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4126394 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4281661 original bottom strand

Deduplication

Alignments analysed 8408055
Unique alignments 6423431
Duplicates removed 1984624
Duplicated alignments were found at 1201335 different positions

Cytosine Methylation after Extraction

Total C's analysed 127237948
Methylated C's in CpG context 5351229
Methylated C's in CHG context 663359
Methylated C's in CHH context 2095978
Unmethylated C's in CpG context 12254820
Unmethylated C's in CHG context 26439097
Unmethylated C's in CHH context 80433465
Percentage methylation (CpG context) 30.4%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.5%

M-Bias Plot