Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3644_14_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_14_R2.fastp-trim.20201206.fq.gz

Data processed at 15:03 on 2021-02-23


Alignment Stats

Sequence pairs analysed in total 36184563
Paired-end alignments with a unique best hit 22562282
Pairs without alignments under any condition 9169795
Pairs that did not map uniquely 4452486
Genomic sequence context not extractable (edges of chromosomes) 2409

Cytosine Methylation

Total C's analysed 792291751
Methylated C's in CpG context 12075264
Methylated C's in CHG context 701440
Methylated C's in CHH context 2955332
Methylated C's in Unknown context 28289
Unmethylated C's in CpG context 88203404
Unmethylated C's in CHG context 137175350
Unmethylated C's in CHH context 551180961
Unmethylated C's in Unknown context 1967195
Percentage methylation (CpG context) 12.0%
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 5615888 original top strand
CTOT 5663921 complementary to original top strand
CTOB 5662867 complementary to original bottom strand
OB 5617197 original bottom strand

Deduplication

Alignments analysed 22559873
Unique alignments 20151779
Duplicates removed 2408094
Duplicated alignments were found at 2137773 different positions

Cytosine Methylation after Extraction

Total C's analysed 484838415
Methylated C's in CpG context 7220083
Methylated C's in CHG context 424785
Methylated C's in CHH context 1792945
Unmethylated C's in CpG context 53754279
Unmethylated C's in CHG context 83253537
Unmethylated C's in CHH context 338392786
Percentage methylation (CpG context) 11.8%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot