Bismark

Bismark Processing Report

/gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF03-EM05-Larvae_R1_001_val_1.fq.gz and /gscratch/scrubbed/samwhite/2018OALarvae_DNAm_discovery/trimmed_files/EF03-EM05-Larvae_R2_001_val_2.fq.gz

Data processed at 00:16 on 2021-05-09


Alignment Stats

Sequence pairs analysed in total 57495743
Paired-end alignments with a unique best hit 17368223
Pairs without alignments under any condition 31935230
Pairs that did not map uniquely 8192290
Genomic sequence context not extractable (edges of chromosomes) 8

Cytosine Methylation

Total C's analysed 543066400
Methylated C's in CpG context 15881566
Methylated C's in CHG context 3354723
Methylated C's in CHH context 16109549
Methylated C's in Unknown context 457080
Unmethylated C's in CpG context 61768028
Unmethylated C's in CHG context 107772983
Unmethylated C's in CHH context 338179551
Unmethylated C's in Unknown context 2506331
Percentage methylation (CpG context) 20.5%
Percentage methylation (CHG context) 3.0%
Percentage methylation (CHH context) 4.5%
Methylated C's in Unknown context N/A%

Alignment to Individual Bisulfite Strands

OT 4316156 original top strand
CTOT 4362907 complementary to original top strand
CTOB 4372137 complementary to original bottom strand
OB 4317015 original bottom strand

Deduplication

Alignments analysed 17368215
Unique alignments 13454927
Duplicates removed 3913288
Duplicated alignments were found at 3027524 different positions

Cytosine Methylation after Extraction

Total C's analysed 236950745
Methylated C's in CpG context 6893130
Methylated C's in CHG context 1561244
Methylated C's in CHH context 7228228
Unmethylated C's in CpG context 26834706
Unmethylated C's in CHG context 46665845
Unmethylated C's in CHH context 147767592
Percentage methylation (CpG context) 20.4%
Percentage methylation (CHG context) 3.2%
Percentage methylation (CHH context) 4.7%

M-Bias Plot