Bismark

Bismark Processing Report

/gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R1_001_val_1.fq.gz and /gscratch/srlab/strigg/data/Pgenr/FASTQS/EPI-205_S26_L004_R2_001_val_2.fq.gz

Data processed at 17:55 on 2018-10-25


Alignment Stats

Sequence pairs analysed in total 10000
Paired-end alignments with a unique best hit 5560
Pairs without alignments under any condition 2442
Pairs that did not map uniquely 1998
Genomic sequence context not extractable (edges of chromosomes) 26

Cytosine Methylation

Total C's analysed 161906
Methylated C's in CpG context 5167
Methylated C's in CHG context 1131
Methylated C's in CHH context 12325
Methylated C's in Unknown context 542
Unmethylated C's in CpG context 17866
Unmethylated C's in CHG context 31647
Unmethylated C's in CHH context 93770
Unmethylated C's in Unknown context 1098
Percentage methylation (CpG context) 22.4%
Percentage methylation (CHG context) 3.5%
Percentage methylation (CHH context) 11.6%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 2342 original top strand
CTOT 435 complementary to original top strand
CTOB 432 complementary to original bottom strand
OB 2325 original bottom strand

Deduplication

Alignments analysed 5534
Unique alignments 5482
Duplicates removed 52
Duplicated alignments were found at 36 different positions

Cytosine Methylation after Extraction

Total C's analysed 114572
Methylated C's in CpG context 3716
Methylated C's in CHG context 868
Methylated C's in CHH context 9505
Unmethylated C's in CpG context 12219
Unmethylated C's in CHG context 21906
Unmethylated C's in CHH context 66358
Percentage methylation (CpG context) 23.3%
Percentage methylation (CHG context) 3.8%
Percentage methylation (CHH context) 12.5%

M-Bias Plot