Bismark

Bismark Processing Report

../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-73-TP2_S7_R1_001.fastq.gz and ../output/01.00-E-Peve-WGBS-trimming-cutadapt-FastQC-MultiQC/trimmed_POR-73-TP2_S7_R2_001.fastq.gz

Data processed at 08:21:36 on 2025-05-01

Alignment Stats

Sequence pairs analysed in total 102561868
Paired-end alignments with a unique best hit 61680314
Pairs without alignments under any condition 29688557
Pairs that did not map uniquely 11192997
Genomic sequence context not extractable (edges of chromosomes) 11356

Cytosine Methylation

Total C's analysed 2962310396
Methylated C's in CpG context 38310421
Methylated C's in CHG context 9626500
Methylated C's in CHH context 43218935
Methylated C's in Unknown context 7482071
Unmethylated C's in CpG context 463611232
Unmethylated C's in CHG context 549194379
Unmethylated C's in CHH context 1858348929
Unmethylated C's in Unknown context 24226368
Percentage methylation (CpG context) 7.6%
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 18614980 original top strand
CTOT 12216738 complementary to original top strand
CTOB 12220945 complementary to original bottom strand
OB 18616295 original bottom strand

Deduplication

Alignments analysed 61668958
Unique alignments 14383247
Duplicates removed 47285711
Duplicated alignments were found at 8503077 different positions

Cytosine Methylation after Extraction

Total C's analysed 449342456
Methylated C's in CpG context 5790052
Methylated C's in CHG context 1701285
Methylated C's in CHH context 8600637
Unmethylated C's in CpG context 69188241
Unmethylated C's in CHG context 81592316
Unmethylated C's in CHH context 282469925
Percentage methylation (CpG context) 7.7%
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 527777209 171827598 30.61 30.52 3.072
T 499383224 171532079 28.96 30.46 2.911
C 334336660 109822870 19.39 19.51 3.044
G 362869409 109866618 21.04 19.51 3.303
AC 97851024 31579141 5.72 5.61 3.099
CA 112460942 36499708 6.57 6.48 3.081
TC 95126986 32794098 5.56 5.82 2.901
CT 96392579 32992892 5.63 5.86 2.922
CC 66662575 22948860 3.90 4.08 2.905
CG 56048612 17370180 3.28 3.09 3.227
GC 72096392 22490193 4.21 3.99 3.206
GG 79099856 22992004 4.62 4.08 3.440
AG 109435314 33058515 6.40 5.87 3.310
GA 108387529 32859848 6.34 5.84 3.298
TG 114975730 36435058 6.72 6.47 3.156
GT 99199001 31514166 5.80 5.60 3.148
TT 170824979 63053650 9.99 11.20 2.709
TA 114713312 39235256 6.71 6.97 2.924
AT 128959593 43957702 7.54 7.81 2.934
AA 188459073 63217613 11.02 11.23 2.981

M-Bias Plot