Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cvirg/3F_R1_val_1.fq.gz and /gscratch/srlab/sr320/data/cvirg/3F_R2_val_2.fq.gz

Data processed at 13:36:55 on 2021-08-12


Alignment Stats

Sequence pairs analysed in total 175332621
Paired-end alignments with a unique best hit 94818304
Pairs without alignments under any condition 56280666
Pairs that did not map uniquely 24233651
Genomic sequence context not extractable (edges of chromosomes) 779

Cytosine Methylation

Total C's analysed 3881124484
Methylated C's in CpG context 59562205
Methylated C's in CHG context 2845441
Methylated C's in CHH context 12466440
Methylated C's in Unknown context 289535
Unmethylated C's in CpG context 453919526
Unmethylated C's in CHG context 696033895
Unmethylated C's in CHH context 2656296977
Unmethylated C's in Unknown context 11856812
Percentage methylation (CpG context) 11.6%
Percentage methylation (CHG context) 0.4%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 23859022 original top strand
CTOT 23742044 complementary to original top strand
CTOB 23539465 complementary to original bottom strand
OB 23676994 original bottom strand

Deduplication

Alignments analysed 94817525
Unique alignments 86601366
Duplicates removed 8216159
Duplicated alignments were found at 7125025 different positions

Cytosine Methylation after Extraction

Total C's analysed 2245598302
Methylated C's in CpG context 33278296
Methylated C's in CHG context 1581182
Methylated C's in CHH context 6889997
Unmethylated C's in CpG context 258732657
Unmethylated C's in CHG context 397571420
Unmethylated C's in CHH context 1547544750
Percentage methylation (CpG context) 11.4%
Percentage methylation (CHG context) N/A%
Percentage methylation (CHH context) N/A%

M-Bias Plot