Table 2 Variant calling metrics of Illumina PCR-free paired-end reads against the assemblies and Illumina PCR-free paired-end reads from Col-0 mapped against the TAIR10 reference assembly
From: High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Name | Round (#) | Total variants (#) | SNPs (#) | Insertions (#) | Deletions (#) |
|---|---|---|---|---|---|
ONTcan | 0 | 2,505,080 | 281,421 | 2,202,363 | 21,296 |
ONTcan | 1 | 1,782,042 | 276,025 | 1,432,415 | 73,602 |
ONTcan | 2 | 1,723,244 | 266,625 | 1,384,435 | 72,184 |
ONTcan | 3 | 1,706,676 | 264,720 | 1,369,595 | 72,361 |
ONTcan | 4 | 99,252 | 73,616 | 10,244 | 15,392 |
ONTmin | 0 | 7,208,897 | 3,359,123 | 2,911,987 | 937,787 |
ONTmin | 1 | 1,994,370 | 345,671 | 1,532,261 | 116,438 |
ONTmin | 2 | 1,767,580 | 287,706 | 1,393,680 | 86,194 |
ONTmin | 3 | 1,730,743 | 278,301 | 1,369,470 | 82,972 |
ONTmin | 4 | 91,544 | 67,062 | 9026 | 15,456 |
PBfal | 0 | 474,355 | 62,063 | 367,338 | 44,954 |
PBfal | 1 | 39,433 | 26,486 | 6860 | 6087 |
PBfal | 4 | 27,312 | 24,744 | 1010 | 1558 |
TAIR10 | – | 16,807 | 13,336 | 1770 | 1121 |
