Table 1.

Size Distribution of Fragments Lost Between Assemblies of Chromosome 10

Fragment length interval (bp)	Percentage of total	Length of largest fragment in interval (bp)	Percentage of interval remapped
30-100	54	99	21
101-200	8	199	29
201-400	15.5	400	16
401-800	15.5	797	14
801-1600	5.3	1507	20
1601-3200	0.5	3008	100
3201-6400	0.6	5789	100
6401-12800	0.5	12293	100
12800+	0.1	21104	100

The fragments included in this distribution were chosen in the following way: the December 2001 assembly of Chromosome 10 was annotated with 18-mer counts within the entire December 2001 assembly as well as within the June 2002 assembly. We stored the coordinates of runs of at least 13 consecutive 18-mers whose counts transitioned from 1 to 0 between assemblies. These 18-mers were further clustered into “dropout fragments” as long as the gaps between them were not greater than 100 bp, and no more than 35% of the fragment length was composed of gaps. A homology search using BLAST was performed to compare the dropout fragments with the vector database; no homology to vector sequence was found. Approximately 800 dropout fragments were found, ranging from 30 bp to 21 kb in length with a combined length of approximately 300 kb.