Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-229_S36_L004_R2_001_val_2.fq.gz

Data processed at 23:49 on 2020-03-24


Alignment Stats

Sequence pairs analysed in total 19891722
Paired-end alignments with a unique best hit 8020238
Pairs without alignments under any condition 9946231
Pairs that did not map uniquely 1925253
Genomic sequence context not extractable (edges of chromosomes) 1

Cytosine Methylation

Total C's analysed 234928287
Methylated C's in CpG context 9402130
Methylated C's in CHG context 1206978
Methylated C's in CHH context 3281401
Methylated C's in Unknown context 62587
Unmethylated C's in CpG context 24903264
Unmethylated C's in CHG context 50373954
Unmethylated C's in CHH context 145760560
Unmethylated C's in Unknown context 512946
Percentage methylation (CpG context) 27.4%
Percentage methylation (CHG context) 2.3%
Percentage methylation (CHH context) 2.2%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 3928266 original top strand
CTOT 0 complementary to original top strand
CTOB 0 complementary to original bottom strand
OB 4091971 original bottom strand

Deduplication

Alignments analysed 8020237
Unique alignments 6036266
Duplicates removed 1983971
Duplicated alignments were found at 1179618 different positions

Cytosine Methylation after Extraction

Total C's analysed 120448317
Methylated C's in CpG context 5162434
Methylated C's in CHG context 610621
Methylated C's in CHH context 1841547
Unmethylated C's in CpG context 11661347
Unmethylated C's in CHG context 24880747
Unmethylated C's in CHH context 76291621
Percentage methylation (CpG context) 30.7%
Percentage methylation (CHG context) 2.4%
Percentage methylation (CHH context) 2.4%

M-Bias Plot