Schmidtea mediterranea

Background:  For this estimated 480 Mb genome, fosmid and plasmid libraries 
were constructed using genomic DNA purified from whole animals of the S2F2 
line, which was clonally derived from a single animal. This unfiltered draft 
assembly contains read pairs from plasmid libraries and a fosmid library 
(only 2254 reads) equivalent to 5.4X sequence coverage of the genome.  Other 
assemblies will follow. This genome has proven to be A/T rich (69%), very 
repetitious (46% of total genome), and heterozygous (even though the animals 
used for DNA preparation were clonally derived) having portions that recombine,
making automated assembly of the genome very difficult. We are now sequencing 
2M reads from a juvenile library to assess whether the apparent heterozygosity 
may reflect recombination found in the adult germline. BAC library preparations
have been unsuccessful, as the DNA degrades during the preparation process.  
The genome size calculated using this assembly is ~1.2 Gb (compared to the 
estimated 480 Mb size).  We are supplying this unfiltered, draft assembly 
to the public, but caveat emptor. 

Assembly Statistics:

Read Numbers:
total reads input: 10,708,032
total reads placed: 7,753,071
total reads unplaced: 2,954,961
chaff rate: 0.28
unplaced reads due to no overlaps found:  11%
unplaced reads are repeats (60%).

Read Quality:
total input phred20 bases: 6,874,953,113
total input reads bases: 8,222,976,099
average phred20 per read: 642.04
average read length: 767.93

Base Content:
total contig length added sum: 1,375,792,741
total major ctg sum: 1,188,208,460

total GC counts in the genome: 429,527,634
total AT counts in the genome: 946,238,125
total NX counts in the genome: 26982

GC%: 31%     
AT%: 69%  

Repeat Content:

Total repeats bases exceed threshold 80 : 3.8G bases
Total reads bases: 8.2G 
 Repeats is about 46.27 % of the total bases

Read Depth:
Average depth of coverage:   5.4 
Phred20 is about 6.78G 
The genome size estimated from redundancy: 1.26G

Mate pair constraints:
No. of satisfied constraints in contigs:     1,554,698
No. of unsatisfied in distance in contigs:     89,125
No. of satisfied links in scaffolds:          444,696
No. of unsatisfied in dist. in scaffolds:      73,182
No. of unsatisfied due to singlets:          2,100,728
No. of unsatisfied due to short scaffolds:    723,804
No. of unsatisfied due to scaffold ends:       14,704
No. of other unsatisfied constraints:          58,355
No. of redundant constraints:                  25,592
Total no. of satisfied constraints:          1,999,394
Total no. of unsatisfied constraints:        3,059,898
Total no. of constraints:                    5,084,884