Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_9_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_9_R2.fastp-trim.20201202.fq.gz

Data processed at 08:32 on 2021-03-03


Alignment Stats

Sequence pairs analysed in total 73776588
Paired-end alignments with a unique best hit 46249576
Pairs without alignments under any condition 18427528
Pairs that did not map uniquely 9099484
Genomic sequence context not extractable (edges of chromosomes) 5273

Cytosine Methylation

Total C's analysed 1614930893
Methylated C's in CpG context 21402276
Methylated C's in CHG context 1304086
Methylated C's in CHH context 5550413
Methylated C's in Unknown context 49721
Unmethylated C's in CpG context 188596358
Unmethylated C's in CHG context 285271601
Unmethylated C's in CHH context 1112806159
Unmethylated C's in Unknown context 3962829
Percentage methylation (CpG context) 10.2%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 11561829 original top strand
CTOT 11578586 complementary to original top strand
CTOB 11565150 complementary to original bottom strand
OB 11538738 original bottom strand

Deduplication

Alignments analysed 46244303
Unique alignments 37981246
Duplicates removed 8263057
Duplicated alignments were found at 6888955 different positions

Cytosine Methylation after Extraction

Total C's analysed 906834456
Methylated C's in CpG context 11638273
Methylated C's in CHG context 720203
Methylated C's in CHH context 3089506
Unmethylated C's in CpG context 104980361
Unmethylated C's in CHG context 158340275
Unmethylated C's in CHH context 628065838
Percentage methylation (CpG context) 10.0%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot