Table 3 Sequencing metrics results for sequenced libraries. Total reads, reads retained after trimming and quality filtering, total number of reads mapping on genomic ntDNA, filtered reads mapping on genomic ntDNA, deduplicated reads mapping on genomic ntDNA, average read length of all retained reads, library clonality as percentage, estimated endogenous DNA content as percentage, GC content of retained reads and estimated library complexity as percentage. Numbers of deduplicated reads mapping on grape mitochondrial MtDNA and Chloroplast CpDNA are given as comparison in the last two columns. Details on samples are provided in TableĀ 1.
From: Optimizing ancient DNA recovery from archaeological plant seeds
Method | Archaeological site | Sample name* | Total reads | Reads filter retained | Mapped reads ntDNA | Mapped reads passed post filter | Deduplicated reads on ntDNA | Average reads length (bp) | Clonality (%) | Endogenous DNA content (%) | GC content (%) | Substitutions 5ā CāT (%) | Complexity (%) | Deduplicated Reads on cpDNA | Deduplicated reads on mtDNA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTAB | Nogara | NG32_A | 9,418,746 | 7,955,455 | 135,480 | 59,802 | 54,772 | 44.3 | 8.4 | 0.8 | 42 | 4 | 91.7 | 727 | 1,632 |
NG35_A | 7,090,304 | 6,264,798 | 201,114 | 99,809 | 91,619 | 46.8 | 8.2 | 1.6 | 40 | 5.2 | 91.9 | 434 | 1,324 | ||
NG38_A | 11,595,140 | 8,572,388 | 276,569 | 117,702 | 105,801 | 39.7 | 10.1 | 1.4 | 42 | 4.5 | 89.9 | 396 | 1,718 | ||
DNeasy | Cologna Veneta | CL104_B | 7,306,282 | 5,980,335 | 309,508 | 154,856 | 144,017 | 69.0 | 6.9 | 2.6 | 41 | 6.6 | 93.0 | 894 | 1,758 |
CL107_B | 9,328,560 | 7,5ā7,551 | 456,524 | 239,209 | 220,419 | 67.5 | 7.9 | 3.2 | 40 | 7.5 | 92.2 | 2,384 | 4,108 | ||
Nogara | NG223_B | 9,476,125 | 7,010,363 | 15,722 | 7,914 | 7,213 | 64.30 | 8.85 | 0.11 | 41 | 5.3 | 91.3 | 89 | 297 | |
S-PDE | Cologna Veneta | CL1_C | 9,127,002 | 8,598,838 | 269,153 | 128,893 | 120,702 | 59.6 | 6.4 | 1.5 | 42 | 8.1 | 93.7 | 4,912 | 27,292 |
CL2_C | 8,021,231 | 7,500,348 | 37,318 | 20,352 | 18,914 | 50.7 | 7.1 | 0.3 | 43 | 9.1 | 93.1 | 316 | 1,007 | ||
CL3_C | 8,596,043 | 8,163,377 | 85,763 | 41,733 | 38,783 | 57.0 | 7.1 | 0.5 | 41 | 9.4 | 93.2 | 1,433 | 2,370 | ||
CL4_C | 10,459,894 | 8,864,789 | 226,562 | 120,232 | 111,394 | 62.8 | 7.4 | 1.4 | 42 | 8.2 | 92.7 | 3,645 | 5,218 | ||
CL7_C | 51,679,107 | 43,076,428 | 828,024 | 452,509 | 444,122 | 53.5 | 1.9 | 1.1 | 40 | 8.0 | 98.5 | 3,183 | 8,904 | ||
CL8_C | 29,904,045 | 25,380,730 | 587,761 | 301,533 | 292,079 | 54.6 | 3.5 | 1.2 | 38 | 6.7 | 96.5 | 12,058 | 40,236 | ||
CL9_C | 41,576,558 | 35,602,912 | 570,639 | 302,519 | 296,408 | 50 | 2.0 | 0.9 | 40 | 9.0 | 86.1 | 11,044 | 15,322 | ||
CL164_C | 3,184,240 | 2,679,637 | 483,232 | 237,373 | 213,996 | 52.0 | 9.9 | 8.9 | 37 | 9.7 | 90.2 | 15,837 | 21,318 | ||
CL165_C | 4,475,113 | 4,282,052 | 77,945 | 41,149 | 36,232 | 53.8 | 11.9 | 0.9 | 36 | 5.6 | 88.1 | 1,178 | 1,457 | ||
CL166_C | 10,602,666 | 8,778,106 | 595,310 | 355,364 | 339,967 | 65.5 | 4.3 | 4.1 | 37 | 9.6 | 95.7 | 6,993 | 9,252 | ||
Nogara | NG6_C | 17,596,280 | 16,538,655 | 37,973 | 22,453 | 21,933 | 40.3 | 2.3 | 0.2 | 42 | 11.9 | 97.7 | 109 | 925 | |
NG11_C | 9,171,013 | 8,524,126 | 110,832 | 57,135 | 52,294 | 47.0 | 8.5 | 0.7 | 41 | 13.3 | 91.5 | 539 | 1,635 | ||
NG13_C | 7,836,054 | 7,138,529 | 193,119 | 92,177 | 84,516 | 49.6 | 8.3 | 1.3 | 41 | 7.2 | 91.7 | 692 | 1,895 | ||
NG14_C | 7,661,824 | 7,023,171 | 134,050 | 64,782 | 60,213 | 50.2 | 7.1 | 0.9 | 41 | 6.5 | 93.0 | 624 | 1,828 | ||
NG29_C | 12,059,669 | 10,837,627 | 160,043 | 83,629 | 80,089 | 47.5 | 4.2 | 0.8 | 38 | 10.1 | 95.8 | 1,538 | 5,161 | ||
NG31_C | 18,600,701 | 15,055,131 | 692,190 | 377,502 | 343,103 | 54.4 | 9.1 | 2.5 | 36 | 14.5 | 93.2 | 15,283 | 39,878 | ||
NG32_C | 7,771,749 | 6,827,623 | 46,292 | 26,334 | 24,919 | 38.8 | 5.4 | 0.4 | 40 | 11.3 | 94.7 | 291 | 1,411 | ||
NG33_C | 13,339,025 | 11,767,167 | 487,116 | 248,227 | 241,832 | 49.9 | 2.6 | 2.1 | 38 | 14.8 | 97.4 | 2,925 | 9,755 |
