Bismark

Bismark Processing Report

../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-140-TP2_S5_R2_001.fastq.gz

Data processed at 20:07:17 on 2025-04-30

Alignment Stats

Sequence pairs analysed in total 253975571
Paired-end alignments with a unique best hit 129549817
Pairs without alignments under any condition 74033883
Pairs that did not map uniquely 50391871
Genomic sequence context not extractable (edges of chromosomes) 223

Cytosine Methylation

Total C's analysed 5587802285
Methylated C's in CpG context 98818956
Methylated C's in CHG context 18036512
Methylated C's in CHH context 87165516
Methylated C's in Unknown context 16505398
Unmethylated C's in CpG context 857492373
Unmethylated C's in CHG context 1013978029
Unmethylated C's in CHH context 3512310899
Unmethylated C's in Unknown context 62100765
Percentage methylation (CpG context) 10.3%
Percentage methylation (CHG context) 1.7%
Percentage methylation (CHH context) 2.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 38859209 original top strand
CTOT 25950331 complementary to original top strand
CTOB 25911923 complementary to original bottom strand
OB 38828131 original bottom strand

Deduplication

Alignments analysed 129549594
Unique alignments 85296883
Duplicates removed 44252711
Duplicated alignments were found at 27014096 different positions

Cytosine Methylation after Extraction

Total C's analysed 2128091197
Methylated C's in CpG context 36773667
Methylated C's in CHG context 7181221
Methylated C's in CHH context 35656246
Unmethylated C's in CpG context 324019082
Unmethylated C's in CHG context 379969323
Unmethylated C's in CHH context 1344491658
Percentage methylation (CpG context) 10.2%
Percentage methylation (CHG context) N/A%
Percentage methylation (CHH context) N/A%

Nucleotide Coverage

Nucleotide Class Counts Sample Counts Genome% in Sample % in Genome fold coverage
A 2572895189 158272347 29.85 30.54 16.256
T 2490459596 157631836 28.89 30.41 15.799
C 1681999059 101422742 19.51 19.57 16.584
G 1875178524 100986991 21.75 19.48 18.569
AC 467028722 28964398 5.47 5.59 16.124
CA 571130098 35119143 6.69 6.78 16.263
TC 490729604 31101682 5.74 6.00 15.778
CT 479265828 30318833 5.61 5.85 15.808
CC 326149103 19974002 3.82 3.85 16.329
CG 289507070 16010751 3.39 3.09 18.082
GC 382148840 21382650 4.47 4.13 17.872
GG 397952360 19929739 4.66 3.85 19.968
AG 552684843 30164497 6.47 5.82 18.322
GA 569333973 30955994 6.66 5.97 18.392
TG 616235061 34881987 7.21 6.73 17.666
GT 501901993 28718592 5.87 5.54 17.477
TT 857457964 57528681 10.04 11.10 14.905
TA 505122980 34119440 5.91 6.58 14.805
AT 627801849 41065624 7.35 7.92 15.288
AA 908829439 58077729 10.64 11.21 15.649

M-Bias Plot