Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg/zr3534_2_R1.fastp-trim.20201202.fq.gz and /gscratch/srlab/sr320/data/cg/zr3534_2_R2.fastp-trim.20201202.fq.gz

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


Alignment Stats

Sequence pairs analysed in total 75413899
Paired-end alignments with a unique best hit 46810182
Pairs without alignments under any condition 19431447
Pairs that did not map uniquely 9172270
Genomic sequence context not extractable (edges of chromosomes) 5626

Cytosine Methylation

Total C's analysed 1630104169
Methylated C's in CpG context 22342159
Methylated C's in CHG context 1396332
Methylated C's in CHH context 5985810
Methylated C's in Unknown context 54371
Unmethylated C's in CpG context 188923130
Unmethylated C's in CHG context 285590712
Unmethylated C's in CHH context 1125866026
Unmethylated C's in Unknown context 4033588
Percentage methylation (CpG context) 10.6%
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 11686394 original top strand
CTOT 11736215 complementary to original top strand
CTOB 11722481 complementary to original bottom strand
OB 11659466 original bottom strand

Deduplication

Alignments analysed 46804556
Unique alignments 38089436
Duplicates removed 8715120
Duplicated alignments were found at 7198771 different positions

Cytosine Methylation after Extraction

Total C's analysed 914393917
Methylated C's in CpG context 12156816
Methylated C's in CHG context 771853
Methylated C's in CHH context 3334418
Unmethylated C's in CpG context 105012145
Unmethylated C's in CHG context 158378687
Unmethylated C's in CHH context 634739998
Percentage methylation (CpG context) 10.4%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot