Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_1_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_1_R2.fastp-trim.20201202.fq.gz

Data processed at 23:58 on 2021-03-12


Alignment Stats

Sequence pairs analysed in total 76522716
Paired-end alignments with a unique best hit 47127724
Pairs without alignments under any condition 17253197
Pairs that did not map uniquely 12141795
Genomic sequence context not extractable (edges of chromosomes) 96

Cytosine Methylation

Total C's analysed 1636781777
Methylated C's in CpG context 22358259
Methylated C's in CHG context 1394261
Methylated C's in CHH context 5914275
Methylated C's in Unknown context 52616
Unmethylated C's in CpG context 191433820
Unmethylated C's in CHG context 285827469
Unmethylated C's in CHH context 1129853693
Unmethylated C's in Unknown context 3992972
Percentage methylation (CpG context) 10.5%
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 11765055 original top strand
CTOT 11788130 complementary to original top strand
CTOB 11797392 complementary to original bottom strand
OB 11777051 original bottom strand

Deduplication

Alignments analysed 47127628
Unique alignments 38388821
Duplicates removed 8738807
Duplicated alignments were found at 7320561 different positions

Cytosine Methylation after Extraction

Total C's analysed 923441134
Methylated C's in CpG context 12160729
Methylated C's in CHG context 771829
Methylated C's in CHH context 3314006
Unmethylated C's in CpG context 106774410
Unmethylated C's in CHG context 159361439
Unmethylated C's in CHH context 641058721
Percentage methylation (CpG context) 10.2%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot