Bismark

Bismark Processing Report

/gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz

Data processed at 23:10:06 on 2021-06-09


Alignment Stats

Sequence pairs analysed in total 100000
Paired-end alignments with a unique best hit 61618
Pairs without alignments under any condition 22474
Pairs that did not map uniquely 15908
Genomic sequence context not extractable (edges of chromosomes) 0

Cytosine Methylation

Total C's analysed 2147800
Methylated C's in CpG context 28863
Methylated C's in CHG context 1776
Methylated C's in CHH context 7687
Methylated C's in Unknown context 61
Unmethylated C's in CpG context 251766
Unmethylated C's in CHG context 374609
Unmethylated C's in CHH context 1483099
Unmethylated C's in Unknown context 5309
Percentage methylation (CpG context) 10.3%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 15265 original top strand
CTOT 15548 complementary to original top strand
CTOB 15353 complementary to original bottom strand
OB 15452 original bottom strand

Deduplication

Alignments analysed 61618
Unique alignments 54892
Duplicates removed 6726
Duplicated alignments were found at 6009 different positions

Cytosine Methylation after Extraction

Total C's analysed 1330789
Methylated C's in CpG context 17210
Methylated C's in CHG context 1071
Methylated C's in CHH context 4667
Unmethylated C's in CpG context 154648
Unmethylated C's in CHG context 229591
Unmethylated C's in CHH context 923602
Percentage methylation (CpG context) 10.0%
Percentage methylation (CHG context) 0.5%
Percentage methylation (CHH context) 0.5%

M-Bias Plot