Table 1. Assignment of supercontigs by chromosome.

Chromosome		Assigned supercontigs			Polymorphisms
Name	Size, kb	Sum, kb	Count	Coverage, %	Count	Per kilobase covered
chr R	2,530	1,743	22	68.9	6,198	3.56
chr 1	3,165	3,034	26	95.9	12,969	4.27
chr 2	2,300	1,989	18	86.5	8,681	4.36
chr 3	1,820	1,666	10	91.6	2,962	1.78
chr 4	1,700	1,485	15	87.4	6,854	4.61
chr 5	1,230	1,081	10	87.9	10,254	9.48
chr 6	1,090	902	12	82.7	6,720	7.45
chr 7	1,020	950	8	93.1	1,640	1.73
Subtotal	14,855	12,851	121	86.5	56,278	4.38
Conflicts		120	2		298	2.48
Unmapped		1,879	143		5,958	3.17
Total	14,855	14,851	266	100.0	62,534	4.21

The haploid supercontig set totals 14,855 kb, which is very close to the estimated haploid genome size derived from physical criteria. Chromosome sizes were calculated from the summation of Sfil fragments assigned to each. The actual size of chr R is ≈ 3.2 Mb; in the table, 700 kb was deducted for its rDNA cluster (measured as BamHI and Xhol fragments). The repeat is present only once in the assembly. The only significant difference from published maps relates to the Sfil fragments of chromosome 1 (24), where fragment J2 appears to be replaced by three small fragments. Also, some Sfil sites that are heterozygous in the mapping strain are absent or present on both homologs in SC5314. “Conflicts” gives statistics for the two PHRAP contigs that contained map markers from more than one chromosome; these contigs were passed unchanged into the diploid assembly. “Unmapped” refers to supercontigs not containing any map markers. Values in the table are rounded.