Table 3 MC-Seq mapping efficiency among tissue and brush swab samples
From: Brush swab as a noninvasive surrogate for tissue biopsies in epigenomic profiling of oral cancer
Name | Mapping efficiency (%) | Difference between swab and tissue (%) | Sequence pairs analyzed in total | Number of paired-end alignments with a unique best hit | Duplicate (%) | Sequence pairs after removing duplicate | Total number of C | Total methylated C’s in CpG context | Total methylated C’s in CHG context | Total methylated C’s in CHH context | CpG with depth coverage > 10x |
|---|---|---|---|---|---|---|---|---|---|---|---|
1C swab | 90.7 | 0.1 | 42,303,352 | 38,369,629 | 52.22 | 18,333,433 | 749,965,581 | 37,720,278 | 2,408,697 | 5,995,678 | 2,738,093 |
1C tissue | 90.6 | Â | 34,732,207 | 31,480,976 | 28.42 | 22,534,549 | 927,088,792 | 44,803,115 | 2,908,059 | 7,258,418 | 2,892,873 |
1 N swab | 89.3 | −0.7 | 35,997,131 | 32,160,165 | 69.49 | 9,811,824 | 392,619,063 | 19,593,941 | 1,231,170 | 3,078,167 | 1,827,202 |
1 N tissue | 90.4 |  | 38,013,580 | 34,357,686 | 50.99 | 16,840,023 | 701,455,939 | 36,205,354 | 2,320,490 | 5,789,438 | 2,671,771 |
2C swab | 91.0 | 1.7 | 49,206,194 | 44,795,293 | 54.25 | 20,495,859 | 825,691,357 | 41,320,643 | 2,723,999 | 6,792,423 | 2,826,344 |
2C tissue | 89.3 | Â | 48,990,997 | 43,728,505 | 39.71 | 26,364,632 | 1,095,985,402 | 53,089,834 | 3,494,884 | 8,728,001 | 3,092,966 |
2 N swab | 86.7 | −1.9 | 40,037,338 | 34,712,643 | 48.22 | 17,975,067 | 745,570,397 | 35,629,449 | 2,300,915 | 5,877,073 | 2,662,761 |
2 N tissue | 88.6 |  | 37,524,719 | 33,261,053 | 48.50 | 17,128,931 | 713,630,671 | 35,589,419 | 2,277,861 | 5,673,182 | 2,685,042 |
3C swab | 90.7 | −0.8 | 36,703,056 | 33,280,675 | 26.89 | 24,331,566 | 1,000,848,080 | 50,517,501 | 3,160,407 | 7,841,535 | 3,017,937 |
3C tissue | 91.5 | Â | 39,728,186 | 36,357,410 | 28.90 | 25,848,885 | 1,069,409,107 | 52,603,435 | 3,264,928 | 8,042,519 | 3,100,471 |
3 N swab | 88.3 | −1.8 | 52,334,030 | 46,226,126 | 34.76 | 30,156,313 | 1,221,133,676 | 62,639,138 | 3,840,377 | 9,388,785 | 3,227,707 |
3 N tissue | 90.1 |  | 41,553,671 | 37,445,490 | 39.68 | 22,588,890 | 950,370,928 | 50,055,981 | 3,072,187 | 7,486,332 | 2,982,445 |
Average swab | 89.45 | −0.567 | 42,763,517 | 38,257,422 | 48.00 | 20,184,010 | 822,638,026 | 41,236,825 | 2,610,928 | 6,495,610 | 2,716,674 |
Average tissue | 90.00 | Â | 40,090,560 | 36,105,187 | 39.00 | 21,884,318 | 909,656,807 | 45,391,190 | 2,889,735 | 7,162,982 | 2,904,261 |