Table 1.

Comparison of main assembly characteristics and quality metrics.

	EGYPT	EGYPT_wtdbg2	EGYPT_falcon	AK1	YORUBA
Assembly level	meta	contig	scaffold	scaffold	chromosome
Effective genome size	2,820,489,739	2,733,934,177	2,897,551,797	NA	NA
# Sequences	3235	3106	1615	2832	1647
Longest sequence	88,566,048	88,566,048	84,324,762	113,921,103	248,986,603
# N’s per 100 kbp	0	0	209.01	1285.7	7180.2
Base level QV	42.4	42.9	43.0	50.4a	NA
# Genes (thereof # partial)	20,908 (3226)	20,613 (3229)	21,176 (1578)	21,047 (1396)	21,077 (1721)
Genome fraction w.r.t. GRCh38 (%)	94.174	92.247	95.924	95.177	95.391
Duplication ratio w.r.t. GRCh38	1.01	0.999	1.018	1.023	1.088
Largest GRCh38 alignment	75,492,126	75,492,126	56,458,009	58,219,133	65,512,502
Total GRCh38 aligned length	2,800,100,449	2,713,712,375	2,865,356,241	2,829,006,639	2,832,740,986
NG50 w.r.t. GRCh38	20,857,787	20,857,787	28,071,354	39,609,866	145,208,384
LG50 w.r.t. GRCh38	35	35	33	24	9
NGA50 w.r.t. GRCh38	11,187,777	11,187,777	8,226,500	13,028,687	19,529,238
LGA50 w.r.t. GRCh38	71	71	95	66	43
# GRCh38 differences >1 kb (thereof # outside centromeres)	1276 (1103)	1276 (1103)	3499 (2832)	1952 (1685)	1756 (1472)
# GRCh38 mismatches per 100 kbp	139	138.72	143.64	126.92	141.56
# GRCh38 indels per 100 kbp	32.09	31.74	40.06	32.77	46.95
K-mer-based compl. w.r.t. GRCh38 (%)	86.01	85.15	87.75	87.68	85.82

The table lists the final EGYPT meta assembly, the two alternative base assemblies EGYPT_wtdbg2 and EGYPT_falcon and two publicly available assemblies of the genomes of a Korean (AK1) and Yoruba individual (YORUBA). Metrics were largely obtained with QUAST-LG. The complete QUAST-LG report and additional assembly metrics are provided in Supplementary Data 2.

^aBased on error rate estimated by AK1 authors Seo et al.¹⁶.