Q1. Reads: 2*1408847 = 2,817,694; Bases: 281Mb
Q2. Avg k-mer coverage ~ 41; Yes 41 > 15.
Q3. Scaffolds: 142, Contigs: 409, Scaffold N50: 377249, Contig N50: 66444
Q4. Yes
Q5. ST-313
Q6. Around 98%
Q7. 104321 reads are duplicates
Q8. 31 variants was called, 8 are indels.
Q9. 19 SNPs that pass all filters
Q10. Because haploid genomes only have 1 copy of each chromosome - therefore heterozygote calls are mapping/sequencing errors
Q11. Our strain is the closest to "B". A Congo 2002 strain of Salmonella Typhimurium ST313.
Q12. 14 of the 19 overlap. Even though this strain is the closest one, there are still some differences so they are not identical.
Q13. Aminoglycoside, Beta-lactam, Phenicol, Sulphonamid and Trimethoprim