Bismark

Bismark Processing Report

../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-173-TP2_S4_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 213856184
Paired-end alignments with a unique best hit 108437982
Pairs without alignments under any condition 60420323
Pairs that did not map uniquely 44997879
Genomic sequence context not extractable (edges of chromosomes) 149

Cytosine Methylation

Total C's analysed 4684212694
Methylated C's in CpG context 76855937
Methylated C's in CHG context 14470774
Methylated C's in CHH context 69704529
Methylated C's in Unknown context 12705187
Unmethylated C's in CpG context 734021072
Unmethylated C's in CHG context 855050390
Unmethylated C's in CHH context 2934109992
Unmethylated C's in Unknown context 48870104
Percentage methylation (CpG context) 9.5%
Percentage methylation (CHG context) 1.7%
Percentage methylation (CHH context) 2.3%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 31883243 original top strand
CTOT 22449007 complementary to original top strand
CTOB 22363582 complementary to original bottom strand
OB 31742001 original bottom strand

Deduplication

Alignments analysed 108437833
Unique alignments 80603411
Duplicates removed 27834422
Duplicated alignments were found at 19173637 different positions

Cytosine Methylation after Extraction

Total C's analysed 1974259511
Methylated C's in CpG context 31870842
Methylated C's in CHG context 6362507
Methylated C's in CHH context 31300370
Unmethylated C's in CpG context 307993633
Unmethylated C's in CHG context 356628244
Unmethylated C's in CHH context 1240103915
Percentage methylation (CpG context) 9.4%
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 2527860556 158272347 29.58 30.54 15.972
T 2465976996 157631836 28.86 30.41 15.644
C 1672640076 101422742 19.57 19.57 16.492
G 1878753279 100986991 21.99 19.48 18.604
AC 461110655 28964398 5.45 5.59 15.920
CA 562262930 35119143 6.64 6.78 16.010
TC 489106572 31101682 5.78 6.00 15.726
CT 477125957 30318833 5.63 5.85 15.737
CC 325120418 19974002 3.84 3.85 16.277
CG 291872568 16010751 3.45 3.09 18.230
GC 381338898 21382650 4.50 4.13 17.834
GG 402152190 19929739 4.75 3.85 20.178
AG 549896658 30164497 6.49 5.82 18.230
GA 567943591 30955994 6.71 5.97 18.347
TG 615897275 34881987 7.27 6.73 17.657
GT 503471561 28718592 5.95 5.54 17.531
TT 845337338 57528681 9.98 11.10 14.694
TA 494210248 34119440 5.84 6.58 14.485
AT 615486691 41065624 7.27 7.92 14.988
AA 885622802 58077729 10.46 11.21 15.249

M-Bias Plot