Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3644_11_R1.fastp-trim.20201206.fq.gz and /gscratch/srlab/sr320/data/cg/zr3644_11_R2.fastp-trim.20201206.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 55732442
Paired-end alignments with a unique best hit 34313844
Pairs without alignments under any condition 14305475
Pairs that did not map uniquely 7113123
Genomic sequence context not extractable (edges of chromosomes) 4587

Cytosine Methylation

Total C's analysed 1203987823
Methylated C's in CpG context 16464158
Methylated C's in CHG context 1020445
Methylated C's in CHH context 4398768
Methylated C's in Unknown context 41528
Unmethylated C's in CpG context 137191904
Unmethylated C's in CHG context 209377026
Unmethylated C's in CHH context 835535522
Unmethylated C's in Unknown context 3013713
Percentage methylation (CpG context) 10.7%
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 8563117 original top strand
CTOT 8590546 complementary to original top strand
CTOB 8588367 complementary to original bottom strand
OB 8567227 original bottom strand

Deduplication

Alignments analysed 34309257
Unique alignments 30244124
Duplicates removed 4065133
Duplicated alignments were found at 3556016 different positions

Cytosine Methylation after Extraction

Total C's analysed 722634891
Methylated C's in CpG context 9665871
Methylated C's in CHG context 605782
Methylated C's in CHH context 2620199
Unmethylated C's in CpG context 81795117
Unmethylated C's in CHG context 124554490
Unmethylated C's in CHH context 503393432
Percentage methylation (CpG context) 10.6%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot