. Author manuscript; available in PMC: 2010 Sep 16.

Published in final edited form as: Science. 2010 May 21;328(5981):994–999. doi: 10.1126/science.1183605

Table 1.

Draft assembly metrics, organized by finishing status¹

		Draft			Improved
Number of strains		133			45
Metric	Passing standard	Pass %	Mean	Range	Pass %	Mean	Range
% of the genome included in contigs²	>90%	100%	98.23%	95.1–99.9%	100%	99.91%	98.6–100%
% of the bases greater then 5x read coverage³	>90%	99%	98.90%	80.8–100%	100%	99.35%	98.8–99.6%
Contig N50	>5 KB	100%	102.61 kb	11.12–861.67 kb	100%	517.92 kb	58.03–3472.99 kb
Contig N75	N/a	99%	54.82 kb	4.97–556.76 kb	100%	340.20 kb	30.56–2635.77 kb
Contig N90	N/a	90%	25.54 kb	2.01–240.69 kb	100%	211.51 kb	14.96–2635.77 kb
Scaffold N50²	>20 KB	100%	883.93 kb	50.56–3356.77 kb	100%	606.77 kb	91.71–2898.42 kb
Scaffold N75²	N/a	100%	511.35 kb	24.31–3237.97 kb	100%	378.22 kb	52.32–2391.23 kb
Scaffold N90²	N/a	99%	282.14 kb	11.74–2490.47 kb	100%	226.24 kb	28.67–2391.23 kb
Average contig length	>5 KB	100%	31.52 kb	5.62–180.70 kb	100%	174.70 kb	23.26–1321.04 kb
% of core genes present in gene list	>90%	99%	99.63%	86.4–100%	100%	99.90%	98.5–100%

Based on current assignments. Draft corresponds to Standard or High Quality Draft sequences, with no additional automated or manual attempts to improve assembly, beyond ensuring exclusion of contaminating sequence. Improved columns correspond to Improved-High-Quality-Draft submission, as defined in section 1.3. None of the reference genomes have been improved beyond this grade at this point.

Calculated only for strains with scaffold assemblies submitted to NCBI. The number of strains with scaffold assemblies, by grade: Draft (74), Improved (37).

Per base coverage not available for all reads, for example, those with some draft level of sequencing prior to the Jumpstart initiative or strains where a combination of technologies was used. The number of strains with per base read coverage: Draft (121), Improved (4).