The Drosophila yakuba Tai18E2 strain used in this project was derived from a single inseminated
female captured in the Tai rainforest on the border of Liberia and Ivory Coast by D. Lachaise. 
This line was inbred for 10 generations via full sib matings and the genome sequenced to a depth 
of ~8x using short-insert plasmid libraries and large-insert fosmid libraries.  The paired-end 
plasmid and fosmid reads were assembled using PCAP (Genome Res. 13:2164-70 2003) and then two 
rounds of primer-directed sequence improvement targeted at improving regions of low-quality 
sequence and closing gaps.  The data was re-assembled and supercontigs were assigned to chromosomes
based on their alignment to the D. melanogaster genome.  Inversions based on the D. yakuba assembly
were then introduced and checked against polytene chromosome banding data.  The resulting assembly
was submitted to GenBank under the accession AAEU00000000.  It can also be downloaded from the GSC
ftp site.

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 yakuba genome was provided 
by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).


Production Sequencing statistics:
project: Drosophila_yakuba-7.1
total reads input: 2244660
total reads placed: 2029679
total reads unplaced: 214981
chaff rate: 0.10

total input phred20 bases: 1522591737
estimated genome size: 160000000
total contig length added sum: 162665134
phred20 bases sequence redundancy: 9.52 X
total input reads bases: 1686318108
average phred20 per read: 678.32
average read length: 751.26

total contig number: 13496
maximum contig length: 1458687
major contig (> 1kb) number: 11806

total supercontig number: 8361
maximum supercontig length: 10394945
major supercontig (> 1kb) number: 7035

based on the added contigs sum
contig N50 length:115562, contig N50 number: 276
supercontig N50 length:2455785, supercontig N50 number: 15

total GC counts in the genome: 68773991 percentage: 0.42
total AT counts in the genome: 93891016 percentage: 0.58
total NX counts in the genome: 127
total NX counts in the genome: 127


total mate pairs forward reverse constraints: 842649
total unsatisfied constraints excluding due to singlton, short supercontig, and supercontigs end: 34647
total unsatisfied rate:  4.11 %


No. of satisfied constraints in contigs:      556379
No. of unsatisfied in distance in contigs:      4722
No. of satisfied links in scaffolds:           57521
No. of unsatisfied in dist. in scaffolds:       8833
No. of unsatisfied due to singlets:            96473
No. of unsatisfied due to short scaffolds:     35977
No. of unsatisfied due to scaffold ends:        8027
No. of other unsatisfied constraints:          34647
No. of redundant constraints:                  40070
Total no. of satisfied constraints:           613900
Total no. of unsatisfied constraints:         188679
Total no. of constraints:                     842649