Bismark

Bismark Processing Report

../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_R1_001.fastq.gz and ../output/01.00-D-Apul-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_ACR-150-TP2_S2_R2_001.fastq.gz

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

Alignment Stats

Sequence pairs analysed in total 234083660
Paired-end alignments with a unique best hit 113214924
Pairs without alignments under any condition 73776618
Pairs that did not map uniquely 47092118
Genomic sequence context not extractable (edges of chromosomes) 117

Cytosine Methylation

Total C's analysed 4826708375
Methylated C's in CpG context 89607039
Methylated C's in CHG context 18299207
Methylated C's in CHH context 86677563
Methylated C's in Unknown context 13932902
Unmethylated C's in CpG context 742472247
Unmethylated C's in CHG context 882032802
Unmethylated C's in CHH context 3007619517
Unmethylated C's in Unknown context 48070600
Percentage methylation (CpG context) 10.8%
Percentage methylation (CHG context) 2.0%
Percentage methylation (CHH context) 2.8%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 35012218 original top strand
CTOT 21625620 complementary to original top strand
CTOB 21552127 complementary to original bottom strand
OB 35024842 original bottom strand

Deduplication

Alignments analysed 113214807
Unique alignments 70054746
Duplicates removed 43160061
Duplicated alignments were found at 24340638 different positions

Cytosine Methylation after Extraction

Total C's analysed 1735010006
Methylated C's in CpG context 30722845
Methylated C's in CHG context 6266562
Methylated C's in CHH context 31087883
Unmethylated C's in CpG context 264611417
Unmethylated C's in CHG context 311687978
Unmethylated C's in CHH context 1090633321
Percentage methylation (CpG context) 10.4%
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 2215979340 158272347 29.91 30.54 14.001
T 2130825031 157631836 28.76 30.41 13.518
C 1443474061 101422742 19.48 19.57 14.232
G 1619653681 100986991 21.86 19.48 16.038
AC 402498894 28964398 5.48 5.59 13.896
CA 490037107 35119143 6.67 6.78 13.954
TC 420508677 31101682 5.73 6.00 13.520
CT 410855297 30318833 5.59 5.85 13.551
CC 279915683 19974002 3.81 3.85 14.014
CG 248794870 16010751 3.39 3.09 15.539
GC 326892058 21382650 4.45 4.13 15.288
GG 345993205 19929739 4.71 3.85 17.361
AG 479627596 30164497 6.53 5.82 15.900
GA 494097473 30955994 6.73 5.97 15.961
TG 529746942 34881987 7.21 6.73 15.187
GT 432357363 28718592 5.89 5.54 15.055
TT 728964068 57528681 9.93 11.10 12.671
TA 433362910 34119440 5.90 6.58 12.701
AT 537751797 41065624 7.32 7.92 13.095
AA 782115087 58077729 10.65 11.21 13.467

M-Bias Plot