Bismark

Bismark Processing Report

../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_R1_001.fastq.gz and ../output/01.00-F-Ptuh-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POC-48-TP2_S11_R2_001.fastq.gz

Data processed at 06:14:03 on 2025-05-01

Alignment Stats

Sequence pairs analysed in total 177078360
Paired-end alignments with a unique best hit 104251182
Pairs without alignments under any condition 50943986
Pairs that did not map uniquely 21883192
Genomic sequence context not extractable (edges of chromosomes) 128

Cytosine Methylation

Total C's analysed 4027104417
Methylated C's in CpG context 26211877
Methylated C's in CHG context 14132535
Methylated C's in CHH context 73475503
Methylated C's in Unknown context 12765557
Unmethylated C's in CpG context 639104269
Unmethylated C's in CHG context 772862587
Unmethylated C's in CHH context 2501317646
Unmethylated C's in Unknown context 47337161
Percentage methylation (CpG context) 3.9%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 2.9%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 30528263 original top strand
CTOT 21610628 complementary to original top strand
CTOB 21607059 complementary to original bottom strand
OB 30505104 original bottom strand

Deduplication

Alignments analysed 104251054
Unique alignments 81204290
Duplicates removed 23046764
Duplicated alignments were found at 16555603 different positions

Cytosine Methylation after Extraction

Total C's analysed 1679292915
Methylated C's in CpG context 10788747
Methylated C's in CHG context 5976871
Methylated C's in CHH context 32297468
Unmethylated C's in CpG context 264448343
Unmethylated C's in CHG context 319836726
Unmethylated C's in CHH context 1045944760
Percentage methylation (CpG context) 3.9%
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 2243561916 116613941 29.93 30.97 19.239
T 2178304332 116748546 29.06 31.00 18.658
C 1423624389 71613560 18.99 19.02 19.879
G 1650199535 71603867 22.02 19.01 23.046
AC 399427662 20840071 5.38 5.53 19.166
CA 478154893 24943498 6.44 6.62 19.170
TC 429601935 22924241 5.79 6.09 18.740
CT 423468460 22427370 5.71 5.96 18.882
CC 267415186 13853764 3.60 3.68 19.303
CG 239043933 10388885 3.22 2.76 23.010
GC 311838508 13995432 4.20 3.72 22.281
GG 350704150 13850871 4.73 3.68 25.320
AG 501126308 22410051 6.75 5.95 22.362
GA 516598849 22896723 6.96 6.08 22.562
TG 541002010 24954009 7.29 6.63 21.680
GT 447619546 20860801 6.03 5.54 21.457
TT 734749489 42681247 9.90 11.33 17.215
TA 452557021 26188985 6.10 6.95 17.280
AT 548846336 30779082 7.40 8.17 17.832
AA 778562774 42584672 10.49 11.31 18.283

M-Bias Plot