Table 3.
Summary of next generation sequencing results.
| Parameters | MBE1 | MBE2 | MBE3 | MBE4 | MBE5 | MBE6 | MBE7 | MBE9 | MBE10 | MBE12 | MBE13 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Year of isolation | 2014 | 2014 | 2014 | 2014 | 2014 | 2014 | 2014 | 2014 | 2014 | 2015 | 2015 |
| Governorate | Gharbia | Gharbia | Beheira | Menofia | Gharbia | Beheira | Gharbia | Alexandria | Alexandria | Menofia | Menofia |
| Tissue of isolation | Lung LN | Lung Tissue | Pre-scapular LN | Head LN | Generalized | Retropharyngeal LN | Mesenteric LN | Retro-pharyngeal LN | Mesenteric LN | Mesenteric LN | Mesenteric LN |
| Breed | Cross breed | Cross breed | Holstein | Holstein | Holstein | Holstein | Holstein | Native | Holstein | Native | Native |
| Age in years | 3 | 5 | 3–5 | 5 | 3–5 | >5 | 5 | >5 | 1–3 | >5 | >5 |
| Consensus length (Mbp) | 4.22 | 4.24 | 4.23 | 4.23 | 4.25 | 4.23 | 4.23 | 4.23 | 4.23 | 4.22 | 4.22 |
| % of bases | 97.10 | 97.37 | 97.02 | 97.55 | 97.51 | 97.31 | 97.39 | 96.99 | 97.31 | 96.59 | 96.01 |
| % G + C | 65.48 | 65.55 | 65.52 | 65.52 | 65.55 | 65.51 | 65.49 | 65.51 | 65.53 | 65.55 | 65.55 |
| # of reads | 2652522 | 9724874 | 2190220 | 2546898 | 7073852 | 2381816 | 2412476 | 3250964 | 3342700 | 22446678 | 19454286 |
| Average Coverage | 140.00 | 514.35 | 115.36 | 135.38 | 374.50 | 126.49 | 127.89 | 170.80 | 175.53 | 584.96 | 498.29 |
| % of mapped reads | 95.91 | 96.75 | 96.14 | 97.16 | 97.08 | 96.53 | 96.69 | 95.77 | 96.72 | 96.41 | 95.8 |
| Mean mapped read length | 241.59 | 240.7 | 240.41 | 240.56 | 239.94 | 241.3 | 240.27 | 241.43 | 238.4 | 120.67 | 119.91 |
| Mean paired read distance | 439.76 | 418.69 | 443.67 | 429.86 | 451.43 | 445.05 | 453.91 | 407.74 | 417.31 | 172.10 | 173.46 |
| # of contigs | 90 | 58 | 83 | 73 | 61 | 75 | 83 | 81 | 71 | 85 | 83 |
| N50 | 104531 | 150169 | 119829 | 119870 | 155216 | 117225 | 117190 | 119771 | 118077 | 107878 | 115326 |
| ANI to M. bovis AF2122/97 | 99.96 | 99.95 | 99.96 | 99.96 | 99.96 | 99.97 | 99.95 | 99.95 | 99.96 | 99.95 | 99.95 |
| # of InDels against M. bovis Af2122/97 | 53 | 61 | 53 | 44 | 68 | 51 | 54 | 30 | 27 | 286 | 343 |
| # of SNPs against M. bovis Af2122/97 | 1343 | 1968 | 1561 | 1744 | 2017 | 1597 | 1477 | 1738 | 1937 | 2124 | 2160 |
| Non-synonymous SNP | 815 | 1222 | 984 | 1084 | 1244 | 995 | 919 | 1082 | 1216 | 1303 | 1338 |
| Synonymous SNP | 382 | 592 | 438 | 513 | 617 | 462 | 411 | 505 | 568 | 676 | 685 |
| Intergenic SNP | 146 | 154 | 139 | 147 | 156 | 140 | 147 | 151 | 153 | 145 | 137 |
| dN/dS* | 1.8059 | 1.7800 | 1.7220 | 1.8060 | 1.7798 | 1.7363 | 1.7086 | 1.9140 | 1.9483 | 1.6203 | 1.8364 |
| In-silico Spoligotyping | SB0268 | SB0268 | SB0268 | SB0268 | SB0268 | SB0268 | SB0268 | SB0120 | SB0120 | unreported | unreported |
*Calculations of dN/dS ratio is based on selected 137 virulence related genes listed in Supplemental Table 1.