Table 2 Statistics for genome assembly and annotation of PBN-43 and PBN-126.
From: Two haplotype-resolved telomere-to-telomere genome assemblies of Xanthoceras sorbifolium
PBN-43_hap1 | PBN-43_hap2 | PBN-126_hap1 | PBN-126_hap2 | ||
|---|---|---|---|---|---|
Assembly | Assembly Length (bp) | 467,233,670 | 464,337,492 | 468,926,305 | 465,040,044 |
Contig N50 (bp) | 29,907,139 | 27,116,286 | 22,604,038 | 21,398,156 | |
Scaffold N50 (bp) | 31,760,580 | 31,013,014 | 31,237,015 | 31,222,858 | |
Number of telomeres | 30 | 30 | 30 | 30 | |
Number of centromeres | 15 | 15 | 15 | 15 | |
Number of gaps | 0 | 0 | 0 | 0 | |
Quality Assessment | QV | 67.01 | 66.79 | 67.02 | 66.79 |
Completeness (%) | 85.97 | 86.11 | 86.63 | 86.68 | |
Assembly BUSCOs (%) | 99.01 | 98.82 | 98.95 | 98.89 | |
Annotation BUSCOs (%) | 98.45 | 98.64 | 97.77 | 98.20 | |
LAI | 18.04 | 17.64 | 16.73 | 16.53 | |
NGS reads mapping rates (%) | 99.25 | 99.25 | 99.24 | 99.33 | |
HiFi reads mapping rates (%) | 100.00 | 100.00 | 100.00 | 100.00 | |
Genes and Repetitive Elements Annotation | Number of genes | 35,069 | 35,054 | 35,174 | 35,039 |
Average gene length (bp) | 3,177 | 3,162 | 3,160 | 3,163 | |
GC content (%) | 35.30 | 35.21 | 35.19 | 35.23 | |
Repeat elements content (%) | 67.92 | 67.63 | 67.95 | 67.79 | |
Retroelements (bp) | 196,168,915 | 193,606,048 | 194,035,806 | 194,267,292 | |
SINEs (bp) | 1,320,181 | 1,328,923 | 1,467,265 | 1,458,220 | |
LINEs (bp) | 16,522,509 | 16,549,464 | 12,767,495 | 12,710,649 | |
LTR elements (bp) | 178,326,225 | 175,727,661 | 179,801,046 | 180,098,423 | |
LTR/Copia (bp) | 76,940,797 | 76,208,096 | 82,985,455 | 82,752,361 | |
LTR/Gypsy (bp) | 85,498,030 | 83,807,409 | 80,757,425 | 81,552,819 | |
DNA transposons (bp) | 108,746,338 | 108,494,395 | 113,461,077 | 109,522,539 | |
Rolling-circles (bp) | 980,283 | 1,016,332 | 768,188 | 878,192 | |
Small RNA (bp) | 1,324,369 | 1,330,604 | 1,492,107 | 1,483,634 | |
Simple repeats (bp) | 6,497,623 | 5,920,875 | 5,890,576 | 6,083,144 | |
Low complexity (bp) | 1,017,948 | 1,007,166 | 1,083,071 | 1,075,734 | |
Unclassified (bp) | 5,907,953 | 5,975,165 | 5,646,859 | 5,627,196 | |
Total bases masked | 318,072,017 | 314,764,019 | 319,469,165 | 316,046,662 | |
Functional Annotation | eggNOG-mapper | 29,299 | 29,304 | 29,451 | 29,512 |
InterProScan | 31,202 | 31,117 | 31,289 | 31,292 | |
KEGG | 10,874 | 10,882 | 10,822 | 10,826 | |
NCBI NR | 31,147 | 31,269 | 31,406 | 31,432 | |
Uniprot_sprot | 20,702 | 20,713 | 20,762 | 20,787 | |
Uniprot_trembl | 30,178 | 30,231 | 30,341 | 30,417 | |
Total annotated genes | 32,944 | 32,863 | 33,002 | 32,961 | |
Percentage of annotated genes | 93.94% | 93.75% | 93.82% | 94.07% | |
