Table 2.
Summary statistics for Illumina RNA sequencing data from individual animals.
| Group/Replicate number∗ |
Total number of reads trimmed |
Number of read pairs being mapping |
Total paired reads after mapping |
% Total paired reads after trimming |
Uniquely mapped reads |
% Uniquely mapped reads |
|---|---|---|---|---|---|---|
| Infected 1 | 73,105,634 | 22,810,292 | 25,147,671 | 68.8 | 23,533,313 | 93.58 |
| Infected 2 | 72,155,108 | 23,491,132 | 24,331,988 | 67.44 | 22,701,378 | 93.30 |
| Infected 3 | 68,005,382 | 21,295,316 | 23,355,033 | 68.69 | 21,941,420 | 93.95 |
| Infected 4 | 48,108,726 | 15,062,194 | 16,523,266 | 68.69 | 15,433,817 | 93.41 |
| LAV-vaccinated 1 | 73,973,058 | 24,360,882 | 24,806,088 | 67.07 | 23,253,486 | 93.74 |
| LAV-vaccinated 2 | 63,076,126 | 20,765,850 | 21,155,138 | 67.08 | 19,668,167 | 92.97 |
| LAV-vaccinated 3 | 34,967,370 | 11,169,558 | 11,898,906 | 68.06 | 11,062,093 | 92.97 |
| LAV-vaccinated 4 | 66,996,260 | 21,387,972 | 22,804,144 | 68.08 | 21,282,727 | 93.33 |
| Mycopar-vaccinated 1 | 60,074,726 | 20,141,682 | 19,966,522 | 66.47 | 18,707,059 | 93.69 |
| Mycopar-vaccinated 2 | 70,284,036 | 23,645,792 | 23,319,122 | 66.36 | 21,978,596 | 94.25 |
| Mycopar-vaccinated 3 | 64,746,832 | 21,633,920 | 21,556,456 | 66.59 | 20,141,993 | 93.44 |
| Naive 1 | 73,575,076 | 22,859,182 | 25,357,947 | 68.93 | 23,681,558 | 93.39 |
| Naive 2 | 50,851,250 | 16,107,620 | 17,371,815 | 68.32 | 16,180,977 | 93.14 |
| Naive 3 | 46,913,012 | 15,083,746 | 15,914,633 | 67.85 | 14,815,443 | 93.09 |
| Naive 4 | 34,829,124 | 11,209,870 | 11,809,627 | 67.81 | 10,972,712 | 92.91 |
∗Time when blood samples were taken: Infected: 30 days post-infection; LAV-vaccinated: 30 days post-LAV vaccination; Mycopar-vaccinated: 30 days post-Mycopar vaccination; Naïve:: 30 days post-PBS vaccination.