Table 5 . Sequencing statistics.
| Strain | Average Depth | No. SE | % SE Mapped | No. PE | % PE Mapped | % PE Pairs | Read Length | % Ref. Covered | No. Homozygous SNPs | No. Multi-Allelic SNPs | No. Homozygous Indels |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 106 | 57.74 | 0 | NA | 38170318 | 84 | 97 | 75 | 97 | 23083 | 496 | 2974 |
| 305 | 107.95 | 0 | NA | 62988628 | 94 | 97 | 76 | 95 | 88337 | 1858 | 11242 |
| 309 | 73.5 | 0 | NA | 43519088 | 95 | 96 | 75 | 99 | 12793 | 481 | 1502 |
| 322 | 30.74 | 0 | NA | 39552812 | 94 | 95 | 35 | 95 | 118890 | 23599 | 13171 |
| 821 | 28.6 | 0 | NA | 36997202 | 93 | 94 | 35 | 93 | 163792 | 24554 | 18872 |
| 1211 | 29.85 | 0 | NA | 35860788 | 98 | 98 | 35 | 99 | 10322 | 10171 | 1214 |
| 1303 | 29.93 | 0 | NA | 36903172 | 97 | 96 | 35 | 98 | 42851 | 16505 | 5376 |
| 1363 | 33.71 | 0 | NA | 27162118 | 69 | 97 | 75 | 86 | 145722 | 919 | 21906 |
| 2261 | 73.42 | 0 | NA | 49455190 | 88 | 90 | 76 | 95 | 44123 | 716 | 6019 |
| 3114 | 28.82 | 0 | NA | 35889678 | 95 | 96 | 35 | 98 | 27169 | 13916 | 3783 |
| 3246 | 32.31 | 0 | NA | 39347694 | 99 | 95 | 35 | 99 | 17290 | 4243 | 1992 |
| 3562 | 32.22 | 0 | NA | 39097638 | 98 | 98 | 35 | 96 | 99284 | 7249 | 12009 |
| 3564 | 32.39 | 0 | NA | 39134336 | 98 | 97 | 35 | 98 | 33587 | 14394 | 4221 |
| 3566 | 83.31 | 27708365 | 97 | 69894872 | 98 | 96 | 36 | 99 | 23580 | 13936 | 3195 |
| 3831 | 80.55 | 22353786 | 92 | 72379318 | 99 | 97 | 36 | 99 | 12885 | 10076 | 2022 |
| 3921 | 31.19 | 0 | NA | 38460204 | 96 | 97 | 35 | 96 | 73150 | 7161 | 8564 |
| 7022 | 47.17 | 0 | NA | 55991650 | 97 | 96 | 36 | 97 | 61278 | 17713 | 7634 |
| 7035 | 34.23 | 0 | NA | 90007810 | 52 | 86 | 35 | 99 | 13310 | 5177 | 1557 |
SE, single end reads; PE, paired end reads.