Volume 25, Number 6—June 2019
Research
Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015
Sasan Fereidouni, Graham L. Freimanis, Mukhit Orynbayev, Paolo Ribeca, John Flannery, Donald P. King, Steffen Zuther, Martin Beer, Dirk Höper, Aidyn Kydyrmanov, Kobey Karamendin, and Richard Kock
Table 3
Main results of the k-mer–based approach on the random amplification metatranscriptomic dataset used in an investigation of a mass die-off of saiga antelopes, Kazakhstan, 2015*
| Organism | No. reads (% total reads) |
|||||
|---|---|---|---|---|---|---|
| Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 | |
| Total no. reads | 231,907 | 773,835 | 272,102 | 300,807 | 235,255 | 187,049 |
| Total no. reads passing QC | 109,302 (47.1) | 553,163 (71.48) | 174,613 (64.17) | 233,888 (77.8) | 171,409 (72.86) | 138,292 (73.93) |
| Unclassified/nonmicrobial | 50,478 (46.18) | 343,404 (62.08) | 86,165 (49.35) | 133,456 (57.06) | 57,812 (33.73) | 50,731 (36.68) |
| Virus | 47 (0.03) | 141 (0.03) | 33 (0.03) | 174 (0.05) | 73 (0.04) | 51 (0.04) |
| Pasteurellaceae | 53,097 (48.58) | 129,337 (23.38) | 69,251 (39.66) | 63,817 (27.29) | 93,378 (54.48) | 72,799 (52.64) |
| Pasteurella multocida | 49,844 (45.6) | 115,231 (20.83) | 60,504 (34.65) | 56,775 (24.27) | 86,664 (50.56) | 67,406 (48.74) |
| Alteromondales | 1303 (1.19) | 2690 (0.49) | 35 (0.02) | 499 (0.21) | 32 (0.02) | 51 (0.04) |
| Enterobacteriaceae | 52 (0.05) | 208 (0.04) | 153 (0.09) | 112 (0.05) | 77 (0.04) | 48 (0.03) |
| Haemophilus | 23 (0.02) | 77 (0.01) | 31 (0.02) | 36 (0.02) | 63 (0.04) | 37 (0.03) |
| Betaproteobacteria | 86 (0.08) | 13160 (2.38) | 30 (0.02) | 86 (0.04) | 18 (0.01) | 22 (0.02) |
| Mannheimia | 10 (0.0) | 18 (0.0) | 12 (0.01) | 18 (0.01) | 19 (0.01) | 9 (0.01) |
| Aggregatibacter | 8 (0.0) | 37 (0.0) | 13 (0.0) | 18 (0.0) | 16 (0.0) | 18 (0.01) |
| Klebsiella | 11 (0.0) | 58 (0.01) | 16 (0.0) | 54 (0.01) | 16 (0.0) | 14 (0.0) |
*Only organisms that were identified in all samples and with >10 reads are listed. Samples 2 and 5 were also tested at Friedrich-Loeffler-Institut by using an RNA sequencing protocol. QC, quality control.
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