Bismark

Bismark Processing Report

../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-178-TP2_S1_R2_001.fastq.gz

Data processed at 20:07:18 on 2025-04-30

Alignment Stats

Sequence pairs analysed in total 182967324
Paired-end alignments with a unique best hit 94962955
Pairs without alignments under any condition 47926569
Pairs that did not map uniquely 40077800
Genomic sequence context not extractable (edges of chromosomes) 154

Cytosine Methylation

Total C's analysed 3994751719
Methylated C's in CpG context 70399594
Methylated C's in CHG context 12957412
Methylated C's in CHH context 62458470
Methylated C's in Unknown context 11680962
Unmethylated C's in CpG context 629501595
Unmethylated C's in CHG context 739934104
Unmethylated C's in CHH context 2479500544
Unmethylated C's in Unknown context 43368441
Percentage methylation (CpG context) 10.1%
Percentage methylation (CHG context) 1.7%
Percentage methylation (CHH context) 2.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 27514924 original top strand
CTOT 19970680 complementary to original top strand
CTOB 19958240 complementary to original bottom strand
OB 27518957 original bottom strand

Deduplication

Alignments analysed 94962801
Unique alignments 67976296
Duplicates removed 26986505
Duplicated alignments were found at 17959815 different positions

Cytosine Methylation after Extraction

Total C's analysed 1620640931
Methylated C's in CpG context 27629121
Methylated C's in CHG context 5440088
Methylated C's in CHH context 26859971
Unmethylated C's in CpG context 253590325
Unmethylated C's in CHG context 295890257
Unmethylated C's in CHH context 1011231169
Percentage methylation (CpG context) 9.8%
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 2083253409 158272347 29.63 30.54 13.162
T 2016362470 157631836 28.68 30.41 12.792
C 1370148924 101422742 19.49 19.57 13.509
G 1560678366 100986991 22.20 19.48 15.454
AC 377818088 28964398 5.42 5.59 13.044
CA 460248489 35119143 6.61 6.78 13.105
TC 398000213 31101682 5.71 6.00 12.797
CT 389802573 30318833 5.60 5.85 12.857
CC 265328161 19974002 3.81 3.85 13.284
CG 241353849 16010751 3.46 3.09 15.074
GC 315727071 21382650 4.53 4.13 14.766
GG 334261483 19929739 4.80 3.85 16.772
AG 458001823 30164497 6.57 5.82 15.183
GA 474239482 30955994 6.81 5.97 15.320
TG 510908651 34881987 7.33 6.73 14.647
GT 416196733 28718592 5.97 5.54 14.492
TT 686214488 57528681 9.85 11.10 11.928
TA 403780789 34119440 5.80 6.58 11.834
AT 504014002 41065624 7.24 7.92 12.273
AA 730003485 58077729 10.48 11.21 12.569

M-Bias Plot