Alignment Stats
| Sequence pairs analysed in total |
22411610 |
| Paired-end alignments with a unique best hit |
12539975 |
| Pairs without alignments under any condition |
2872597 |
| Pairs that did not map uniquely |
6999038 |
| Genomic sequence context not extractable (edges of chromosomes) |
1 |
|
|
Cytosine Methylation
| Total C's analysed |
553992854 |
| Methylated C's in CpG context |
13126282 |
| Methylated C's in CHG context |
567072 |
| Methylated C's in CHH context |
2516446 |
| Methylated C's in Unknown context |
66185 |
| Unmethylated C's in CpG context |
54277842 |
| Unmethylated C's in CHG context |
94014164 |
| Unmethylated C's in CHH context |
389491048 |
| Unmethylated C's in Unknown context |
599610 |
| Percentage methylation (CpG context) |
19.5% |
| Percentage methylation (CHG context) |
0.6% |
| Percentage methylation (CHH context) |
0.6% |
| Methylated C's in Unknown context |
9.9% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
6277370 |
original top strand |
| CTOT |
0 |
complementary to original top strand |
| CTOB |
0 |
complementary to original bottom strand |
| OB |
6262604 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
12539974 |
| Unique alignments |
12012233 |
| Duplicates removed |
527741 |
| Duplicated alignments were found at 505077 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
425933672 |
| Methylated C's in CpG context |
10057694 |
| Methylated C's in CHG context |
351795 |
| Methylated C's in CHH context |
1582325 |
| Unmethylated C's in CpG context |
41857386 |
| Unmethylated C's in CHG context |
72344334 |
| Unmethylated C's in CHH context |
299740138 |
| Percentage methylation (CpG context) |
19.4% |
| 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 | 1007515952 | 378413849 | 34.52 | 32.06 | 2.662 |
|---|
| T | 930362164 | 378309330 | 31.87 | 32.05 | 2.459 |
|---|
| C | 465154529 | 211781786 | 15.94 | 17.94 | 2.196 |
|---|
| G | 515819228 | 211810957 | 17.67 | 17.95 | 2.435 |
|---|
| AC | 159531872 | 68264877 | 5.50 | 5.78 | 2.337 |
|---|
| CA | 192172703 | 80836853 | 6.63 | 6.85 | 2.377 |
|---|
| TC | 146583701 | 67705770 | 5.06 | 5.74 | 2.165 |
|---|
| CT | 132500485 | 62481783 | 4.57 | 5.29 | 2.121 |
|---|
| CC | 80565833 | 42358709 | 2.78 | 3.59 | 1.902 |
|---|
| CG | 56369099 | 26104181 | 1.95 | 2.21 | 2.159 |
|---|
| GC | 75122143 | 33452245 | 2.59 | 2.83 | 2.246 |
|---|
| GG | 93726968 | 42378301 | 3.23 | 3.59 | 2.212 |
|---|
| AG | 161475568 | 62424886 | 5.57 | 5.29 | 2.587 |
|---|
| GA | 176945358 | 67679435 | 6.11 | 5.73 | 2.614 |
|---|
| TG | 200559567 | 80903356 | 6.92 | 6.85 | 2.479 |
|---|
| GT | 166357940 | 68300800 | 5.74 | 5.79 | 2.436 |
|---|
| TT | 313084682 | 128294772 | 10.80 | 10.87 | 2.440 |
|---|
| TA | 263416411 | 101400983 | 9.09 | 8.59 | 2.598 |
|---|
| AT | 311913986 | 119230832 | 10.76 | 10.10 | 2.616 |
|---|
| AA | 367630077 | 128492079 | 12.69 | 10.89 | 2.861 |
|---|
|
|
M-Bias Plot
