Q1. BWA
Q2. 1 read is unmapped
Q3. 70 nt
Q3. 4425188/4=1106297 reads
Q4. 77440790/1106297 = 70 (yes)
Q5. 77440790/6588339 = 11.75X
Q6. Less reads, numbers are: 1022512, 1022480, 931806
Q7 and Q8. When we trimmed the reads for quality we got actually got fewer reads that mapped, but the reads that were removed had many mismatches. Having many mismatches in it self is not bad, it may just be divergent from the reference, but when they have bad qualities then they should be removed. They may mess up downstream calculations such as SNP calling.
Q9. No, it is called in a region where there are repeats (ribosomal RNAs). Risk of mapping errors will be fairly large.
Q10. Uneven coverage, missing regions, many SNPs and base-errors
Q11. 41.9% at 10X or more. Around 95% of the genome not covered with any reads 
Q12. 184 missing genes (<50%). Many hypotheticals, bacteriophages, probable proteins
Q13. Yes, they are bacteriocins used for killing other bacteria, why could it have lost these genes?
Q14. A: m=183,s=8.3; B: m=482,s=9.3
Q15. Indels for 454 and Ion Torrent, nice data for Solid