Alignment Stats
| Sequence pairs analysed in total |
41446330 |
| Paired-end alignments with a unique best hit |
23803175 |
| Pairs without alignments under any condition |
4367286 |
| Pairs that did not map uniquely |
13275869 |
| Genomic sequence context not extractable (edges of chromosomes) |
2 |
|
|
Cytosine Methylation
| Total C's analysed |
1047457619 |
| Methylated C's in CpG context |
26326058 |
| Methylated C's in CHG context |
1243346 |
| Methylated C's in CHH context |
5639286 |
| Methylated C's in Unknown context |
152156 |
| Unmethylated C's in CpG context |
101463337 |
| Unmethylated C's in CHG context |
176620425 |
| Unmethylated C's in CHH context |
736165167 |
| Unmethylated C's in Unknown context |
1009112 |
| Percentage methylation (CpG context) |
20.6% |
| Percentage methylation (CHG context) |
0.7% |
| Percentage methylation (CHH context) |
0.8% |
| Methylated C's in Unknown context |
13.1% |
|
|
Alignment to Individual Bisulfite Strands
| OT |
11919458 |
original top strand |
| CTOT |
0 |
complementary to original top strand |
| CTOB |
0 |
complementary to original bottom strand |
| OB |
11883715 |
original bottom strand |
|
|
Deduplication
| Alignments analysed |
23803173 |
| Unique alignments |
22108613 |
| Duplicates removed |
1694560 |
| Duplicated alignments were found at 1579138 different positions |
|
|
Cytosine Methylation after Extraction
| Total C's analysed |
740428889 |
| Methylated C's in CpG context |
18544364 |
| Methylated C's in CHG context |
769395 |
| Methylated C's in CHH context |
3528064 |
| Unmethylated C's in CpG context |
71950973 |
| Unmethylated C's in CHG context |
124900286 |
| Unmethylated C's in CHH context |
520735807 |
| Percentage methylation (CpG context) |
20.5% |
| 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 | 1888432987 | 378413849 | 34.69 | 32.06 | 4.990 |
|---|
| T | 1734017014 | 378309330 | 31.85 | 32.05 | 4.584 |
|---|
| C | 864478416 | 211781786 | 15.88 | 17.94 | 4.082 |
|---|
| G | 957366201 | 211810957 | 17.58 | 17.95 | 4.520 |
|---|
| AC | 296445542 | 68264877 | 5.48 | 5.78 | 4.343 |
|---|
| CA | 357711511 | 80836853 | 6.62 | 6.85 | 4.425 |
|---|
| TC | 272505282 | 67705770 | 5.04 | 5.74 | 4.025 |
|---|
| CT | 245570516 | 62481783 | 4.54 | 5.29 | 3.930 |
|---|
| CC | 149586749 | 42358709 | 2.77 | 3.59 | 3.531 |
|---|
| CG | 104940697 | 26104181 | 1.94 | 2.21 | 4.020 |
|---|
| GC | 139662293 | 33452245 | 2.58 | 2.83 | 4.175 |
|---|
| GG | 174558117 | 42378301 | 3.23 | 3.59 | 4.119 |
|---|
| AG | 299699584 | 62424886 | 5.54 | 5.29 | 4.801 |
|---|
| GA | 330038671 | 67679435 | 6.11 | 5.73 | 4.876 |
|---|
| TG | 371300223 | 80903356 | 6.87 | 6.85 | 4.589 |
|---|
| GT | 306100632 | 68300800 | 5.66 | 5.79 | 4.482 |
|---|
| TT | 587067431 | 128294772 | 10.86 | 10.87 | 4.576 |
|---|
| TA | 490733513 | 101400983 | 9.08 | 8.59 | 4.840 |
|---|
| AT | 583162908 | 119230832 | 10.79 | 10.10 | 4.891 |
|---|
| AA | 696161435 | 128492079 | 12.88 | 10.89 | 5.418 |
|---|
|
|
M-Bias Plot
