Bismark

Bismark Processing Report

../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-145-TP2_S3_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 244866108
Paired-end alignments with a unique best hit 128317307
Pairs without alignments under any condition 64999585
Pairs that did not map uniquely 51549216
Genomic sequence context not extractable (edges of chromosomes) 139

Cytosine Methylation

Total C's analysed 5649675342
Methylated C's in CpG context 85511979
Methylated C's in CHG context 18977692
Methylated C's in CHH context 88350399
Methylated C's in Unknown context 16139487
Unmethylated C's in CpG context 878134725
Unmethylated C's in CHG context 1019570879
Unmethylated C's in CHH context 3559129668
Unmethylated C's in Unknown context 58014953
Percentage methylation (CpG context) 8.9%
Percentage methylation (CHG context) 1.8%
Percentage methylation (CHH context) 2.4%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 38248879 original top strand
CTOT 26115718 complementary to original top strand
CTOB 25906262 complementary to original bottom strand
OB 38046309 original bottom strand

Deduplication

Alignments analysed 128317168
Unique alignments 61132338
Duplicates removed 67184830
Duplicated alignments were found at 27889563 different positions

Cytosine Methylation after Extraction

Total C's analysed 1643141123
Methylated C's in CpG context 24058487
Methylated C's in CHG context 5731243
Methylated C's in CHH context 27817483
Unmethylated C's in CpG context 252224414
Unmethylated C's in CHG context 289137573
Unmethylated C's in CHH context 1044171923
Percentage methylation (CpG context) 8.7%
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 1910471498 158272347 30.19 30.54 12.071
T 1824584651 157631836 28.83 30.41 11.575
C 1235209439 101422742 19.52 19.57 12.179
G 1358928432 100986991 21.47 19.48 13.456
AC 348978975 28964398 5.56 5.59 12.049
CA 424505497 35119143 6.77 6.78 12.088
TC 359842676 31101682 5.73 6.00 11.570
CT 350479508 30318833 5.59 5.85 11.560
CC 238841080 19974002 3.81 3.85 11.958
CG 210201051 16010751 3.35 3.09 13.129
GC 276568677 21382650 4.41 4.13 12.934
GG 287626796 19929739 4.58 3.85 14.432
AG 404011976 30164497 6.44 5.82 13.394
GA 415061277 30955994 6.61 5.97 13.408
TG 444390226 34881987 7.08 6.73 12.740
GT 363087232 28718592 5.79 5.54 12.643
TT 628748151 57528681 10.02 11.10 10.929
TA 376911068 34119440 6.01 6.58 11.047
AT 465603563 41065624 7.42 7.92 11.338
AA 680073976 58077729 10.84 11.21 11.710

M-Bias Plot