The Drosophila simulans genome project involved light WGS sequencing of 
seven highly inbred strains; white501, C167.4, New Caledonia, Inbred4, Inbred6, 
MD199S and MD106TS, with on strain, w501, receiving higher coverage than the 
others  

Embryo DNA was isolated from the w501 strain and sequenced to a depth of 
3.8X (3.1X in plasmids plus 0.7X in fosmids).  The reads were assembled using 
PCAP (Genome Res. 13(9):2164-70 2003) for an assembled coverage of 2.43X 
in plasmids and 0.48X in fosmids, for a total coverage of 2.91X.  Chromosomal 
assignments made by alignment to the D. melanogaster genome (release 4.0), 
incorporating inversions defined by the assembly and confirmed by comparison 
to polytene chromosome band location.  This assembly can be retrieved from 
GenBank (http://www.ncbi.nlm.nih.gov/) under the accession AAGH01000000.

DNA was isolated from adults for five of the other six strains.  For one strain, 
MD199S, DNA was isolated only from adult females to facilitate assembly of the 
D. simulans Y chromosome.  Each strain was sequenced to a depth ~1X and 
assembled using PCAP.  

A D. simulans assembly representing a mosaic of several different D. simulans 
lines was constructed.  The assembly process began with a ~3X WGS assembly 
of the the D. simulans w501 line.  The w501 contigs were initially anchored, 
ordered and oriented by alignment with the D. melanogaster genome. The 
assembly was then examined for places where the w501 assembly suggested 
inversions with respect to the D. melanogaster assembly. One major inversion 
was found, confirming the already documented inversion found by Lemeunier 
and Ashburner (Proc R Soc Lond B Biol Sci. 1976).  Six other ~1X coverage D. 
simulans lines (c167.4, md106ts, md199s, nc48s, sim4, and sim6) were 
assembled. Using the 4X WGS assembly of the w501 genome as a scaffold, 
contigs and unplaced reads from the 1X assemblies of the other individual strains 
were used to cover gaps in the w501 assembly where possible. Thus the 
resulting assembly is a mosaic containing the w501 contigs as the primary 
scaffolding with contigs and unplaced reads from the other lines filling gaps in 
the w501 assembly.

For answers to questions about this assembly or project, or any other GSC genome
project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) 
and email the designated contact person.

Funding for the sequence characterization of the Drosophila simulans genome was provided 
by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

Production Sequencing statistics:

project: Drosophila_simulans_w501-1.1

** SIMPLE READ STATS ***
total reads input : 637022
total reads placed:   576740
total reads unplaced:    60282
chaff rate : 0.09

total input phred20 bases = 437057720
total contig length added sum (estimated genome size) = 125683891
phred20 sequence redundancy: 3.48 X
total contig number: 31198
maximum contig length: 66623
major contig (> 1kb) number: 27815

total supercontig number: 10765
maximum supercontig length: 4729806
major supercontig (> 1kb) number: 8242

contig N50 length:7074, contig N50 number:4981
supercontig N50 length:793303, supercontig N50 number:35

total GC counts in the genome: 53364753
total AT counts in the genome: 72313667
total NX counts in the genome: 5471


total mate pairs forward reverse constraints: 310177
total unsatisfied constraints excluding due to singleton, short supercontig, and supercontigs end: 7360
total unsatisfied rate:  2.37 %
No. of satisfied constraints in contigs:      134487
No. of unsatisfied in distance in contigs:      2671
No. of satisfied links in scaffolds:           93894
No. of unsatisfied in dist. in scaffolds:       5304
No. of unsatisfied due to singlets:            41049
No. of unsatisfied due to short scaffolds:     23762
No. of unsatisfied due to scaffold ends:        1650
No. of other unsatisfied constraints:           7360
No. of redundant constraints:                      0
Total no. of satisfied constraints:           228381
Total no. of unsatisfied constraints:          81796
Total no. of constraints:                     310177