Table 1. Comparison of selected assemblies.

Statistic	Notes	Assembly
Assembly	a	WGA	CSA	HG06	WGSA	NCBI-28	NCBI-34
Producer	b	Celera	Celera	UCSC	Celera	NCBI	NCBI
Method	c	WG	C	H	WG	H	H
Data source	d	Combined	Combined	IHGSC	Celera	IHGSC	IHGSC
Associated date	e	Nov. 2000	Jan. 2001	Dec. 2000	Dec. 2001	Dec. 2001	Oct. 2003
Intrinsic measures
acgt in assembly, Mbp	f	2,587	2,656	2,742	2,696	2,853	2,865
acgt unmapped, Mbp	g	280	60	37	36	58	22
No. of contigs	h	221,036	169,157	133,667	211,493	47,117	512
No. of scaffolds	i	118,968	54,061	76,058	4,940	42,754	447
N50 contig length, kbp	j	53	98	110	23	575	29,105
N50 scaffold length, kbp	j	3,563	2,954	331	29,133	613	36,791
Scaffold span, Mbp	k	2,848	2,909	2,833	2,819	2,855	2,869
RefSeq (50% cov, 95% id)	l	17,348	18,305	18,122	19,149	18,810	19,613
Segmental duplication, Mbp	m	27.3	54.5	108.0	69.5	120.0	152.3
Seg. dup. in unmapped, Mbp	n	13.9	5.1	2.9	8.3	2.7	5.1
Confirmed conflicted mates	o	0.38%	0.91%	5.61%	0.31%	2.44%	0.28%
Mates linking mapped + unmapped	p	1.52%	0.16%	0.03%	0.13%	0.02%	0.01%
Comparison to NCBI-34
No. of matches	q	256,021	208,148	150,624	308,371	60,544
No. of runs	q	12,560	47,540	71,291	7,315	23,024
No. of clumps	q	1,595	1,187	3,189	339	2,951
acgt in matches, Mbp	r	2,498	2,520	2,495	2,657	2,653
Extra sequence, Mbp	s	89	136	247	38	200
Missing sequence, Mbp	t	367	345	370	208	212
acgt in runs, Mbp	u	2,557	2,650	2,553	2,759	2,682
N50 match length, kbp	v	27	33	47	15	306
N50 run length, kbp	v	1,204	441	203	1,959	954
N50 clump length, kbp	v	5,404	5,931	1,809	33,501	2,765
Percent of acgt in matches to NCBI-34 in:
Global HCS	w	79.86%	78.65%	72.73%	95.96%	77.35%
Unmapped scaffolds	x	8.76%	1.50%	0.78%	0.78%	0.41%
Mismapped scaffolds	y	10.69%	18.41%	17.14%	2.45%	21.11%
Scaffold-incompat. matches	z	0.68%	1.44%	9.35%	0.81%	1.12%
Potentially chimeric scaffolds	aa	9	33	666	25	97
Chimeric acgt, Mbp	bb	10	27	112	13	21
No. of small conflicts	cc	3,474	6,165	14,582	3,912	1,586
acgt in small conflicts, Mbp	dd	7	9	121	8	9

More extensive results are contained in Tables 3 and 8 and Data Set 8 on the PNAS web site.

^aAssembly gives the acronym used in the text.

^bProducers are Celera (www.celeradiscoverysystem.com), University of California, Santa Cruz (UCSC, www.genome.ucsc.edu), and NCBI (www.ncbi.nlm.nih.gov).

^cMethod identifies the computational approach used to produce each assembly: WG, whole-genome; C, compartmental; H, hierarchical.

^dData sources are Celera (shotgun reads plus public BAC ends), IHGSC (HGP data), or a combination (Celera data plus a subset of human genomic data from GenBank).

^eDates shown are assembly completion date (Celera), data freeze date (UCSC), or release date (NCBI).

^fUnambiguous bases in the assembly consensus sequence (including “acgt unmapped”).

^gUnambiguous bases not assigned to specific chromosome locations.

^hContiguous sequence built of overlapping sequencing reads.

ⁱChains of linked contigs.

^jA base has a 50% chance of being in a contig or scaffold at least this long.

^kSum of the lengths of the scaffolds, including internal Ns.

^lRefSeqs alignable at 50% coverage and 95% identity thresholds.

^mBases in matches to segmental duplications in NCBI-34.

ⁿSubset of segmental duplication unmapped in this assembly.

^oPercent of mate pairs indicating a possible misassembly. Mate pair data indicate relative orientation and distance between pairs of sequencing reads. Celera fragments were aligned to each assembly. Where two or more pairs of fragments imply the same rearrangement, they are counted as a possible misassembly.

^pPercent of aligned mate pairs with one fragment aligned to an unmapped scaffold (see “acgt unmapped”) while the other is aligned to a mapped scaffold.

^qAnalysis of A2Amapper's one-to-one mapping between each assembly and NCBI-34. Matches, runs, and clumps are successively less restrictive local alignments, derived from the one-to-one mapping, as described in the text. Informally, matches never include gaps > 10 bp, runs never span conflicting matches, and clumps never span a conflict >50 kbp.

^rUnambiguous bases within matches.

^sUnambiguous bases of each assembly outside all matches.

^tUnambiguous bases of NCBI-34 outside matches to this assembly.

^uUnambiguous NCBI-34 bases within runs.

^vA matched base has a 50% chance of being in a match/run/clump at least this long.

^wPercent of matched bases in the maximal set of consistent matches, defined by heaviest common subsequence (HCS).

^xPercent of matched bases in unmapped scaffolds.

^yPercent bases in matches in scaffolds disagreeing with NCBI-34 in chromosome assignment, order, or orientation.

^zPercent of matched bases in scaffold-incompatible matches, where a match is incompatible with its scaffold if it conflicts with the (length-weighted) majority of matches in the scaffold.

^aaScaffolds with a consistent subset of incompatible matches >50 kb.

^bbUnambigous bases in minority subset(s) for potentially chimeric scaffolds.

^ccRuns of incompatible matches not counted in “Potentially chimeric scaffolds.”

^ddUnambigous bases in matches in small conflicts.