Table 2 Metrics of the R. kirilowii xh-4 genome assembly.
From: Chromosome-level genome and annotation of the tetraploid Rhodiola kirilowii
Genomic features | Hap1 | Hap2 | Hap3 | Hap4 | xh-4.v1 | |
|---|---|---|---|---|---|---|
Assembly statistics | Total size (Mb) | 572.37 | 511.99 | 527.08 | 560.62 | 1922.78 |
Number of contigs | 2635 | 2179 | 2150 | 2515 | 9015 | |
Max contig length (Mb) | 31.62 | 31.62 | 31.62 | 31.62 | 31.62 | |
N50 contig length (Mb) | 0.537 | 0.523 | 0.552 | 0.504 | 0.474 | |
N50 contig | 196 | 209 | 205 | 231 | 943 | |
Number of scaffolds | 11 + 1* + 474** | 11 | 11 | 11 | 519 | |
NG50 scaffold length (Mb) | 51.39 | 45.38 | 45.17 | 54.07 | 46.03 | |
GC% | 40.47 | 40.42 | 40.37 | 40.4 | 40.31 | |
Merqury | Quality | 34.28 | 34.67 | 34.6 | 34.27 | 34.1 |
Error | 0.00037 | 0.00034 | 0.00034 | 0.00037 | 0.00038 | |
Assembly-BUSCO | Complete and single-copy (%) | 60.8 | 68.6 | 65.9 | 66.3 | 4.7 |
Complete and duplicated (%) | 34.1 | 23.5 | 23.1 | 23.9 | 94.5 | |
Fragmented (%) | 0.4 | 0.4 | 0.8 | 1.2 | 0.8 | |
Missing (%) | 4.7 | 7.5 | 10.2 | 8.6 | 0 | |
Protein-coding genes | 26,849 | 25,446 | 26,830 | 28,034 | 122,035 | |
Repeats | Total size (Mb) | 350.77 | 312.57 | 354.09 | 340.82 | 1230.94 |
% of genome | 61.17 | 60.92 | 61.75 | 60.66 | 63.88 | |
Annotation-BUSCO | Complete and single-copy (%) | 56.9 | 53.3 | 50.6 | 54.9 | 1.6 |
Complete and duplicated (%) | 31.8 | 30.2 | 30.6 | 29 | 97.3 | |
Fragmented (%) | 2 | 2 | 3.1 | 2.4 | 0 | |
Missing (%) | 9.3 | 14.5 | 15.7 | 13.7 | 1.1 | |
Illumina Mapping | % of mapped reads | 94.93 | 95.60 | 95.21 | 95.75 | 99.15 |
General mismatch rate | 0.02 | 0.02 | 0.02 | 0.02 | 0.0067 | |
Mean mapping quality | 28.2181 | 32.7356 | 32.7074 | 32.4369 | 18.5344 | |
