Bismark

Bismark Processing Report

/gscratch/scrubbed/sr320/0924/EPI-151_S2_L002_R1_001_val_1.20bp-trim.fq.gz and /gscratch/scrubbed/sr320/0924/EPI-151_S2_L002_R2_001_val_2.20bp-trim.fq.gz

Data processed at 07:08 on 2019-09-26


Alignment Stats

Sequence pairs analysed in total 24493406
Paired-end alignments with a unique best hit 9735627
Pairs without alignments under any condition 12299173
Pairs that did not map uniquely 2458606
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 238015641
Methylated C's in CpG context 8357504
Methylated C's in CHG context 650086
Methylated C's in CHH context 2439382
Methylated C's in Unknown context 25289
Unmethylated C's in CpG context 23921725
Unmethylated C's in CHG context 50258052
Unmethylated C's in CHH context 152388892
Unmethylated C's in Unknown context 480225
Percentage methylation (CpG context) 25.9%
Percentage methylation (CHG context) 1.3%
Percentage methylation (CHH context) 1.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4781374 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4954253 original bottom strand

Deduplication

Alignments analysed 9735627
Unique alignments 7070246
Duplicates removed 2665381
Duplicated alignments were found at 1650571 different positions

Cytosine Methylation after Extraction

Total C's analysed 119614793
Methylated C's in CpG context 4250403
Methylated C's in CHG context 282759
Methylated C's in CHH context 1268204
Unmethylated C's in CpG context 11097048
Unmethylated C's in CHG context 24489654
Unmethylated C's in CHH context 78226725
Percentage methylation (CpG context) 27.7%
Percentage methylation (CHG context) 1.1%
Percentage methylation (CHH context) 1.6%

M-Bias Plot