1> all the stuff and work here is just an ok to be considered, and we got two piles of PCR result in large quantity, which reduces the number of contigs below to 1000 already.
2>another PCR is on the way and the order of contigs becomes clear increasingly. thus the next step will focus on the PCR to fill the gaps.
i can feel that the number will reduce day by day until 300, because we estimated that number by blocks even in accord with the experiment assemblying the consesus sequences by thier overlap fragment.
3> as for the coverage problem, i think it is a huge problem not just for the total DNA.  Actually the unbalance between multiple copy plasminds and chromosome DNA palys the key role in this project. Frankly we have sequence the those plasmids for over 35coverages (for example pBMB9741 over 50 coverages)  but for the chromosome DNA we just do for more or less 6 coverage. It is not the common abundance Mr. Bao said before that can be explained for this genome sequence problem.
4>this genome have many repeat cases so, it raises the difficulty of assembly. As far as i am concerned, the question is out way of that level. Several days ago i kept asking Mr Sun the fragment's location in the chromosome or free, since i was confussed by sth looking right. AT PRESENT I HAVE SOME IDEA ABOUT THAT, you see THE LIMITATION OF SEQUENCE IS 500bp,  but THE POSSIBLE REPEAT OR HOMO FRAGMENTS IN THIS GENOME ARE MAYBE OVER 1000bp, so we saw many wrong assembly cases.
5> after I have ever done the diffrent data assembly experiments, the data would raise the good unexpected features. i am now checking those
results. perhaps it will bring us the bright things. But  the possible undermine is sure, i will deal with them carefully.
6> i am alway thinking that Mr Bao thinks this genome project down, and it is not an easy job for just doing,doing and no question. What we see is that result of YBT1520, why it looks in that way? There must be sth that caused it. Clear our mind,not be blind again and do the work intensively, we will find our successful way.
bless us..  Tony  Hangzhuo