Table 3.
Summary of sequencing and assembly data of five samples that were identified to have mixed populations of Newcastle disease virus (NDV) and other avian viruses
| Isolate number | % PF readsa | Number of raw read pairs | Number of filtered read pairsb | Forward read qualityc | Reverse read qualityc | Identified virus | Final coverage depthc | Number of reads used for consensusd | Consensus nucleotide length | Missing positions at 5' ende | Length of internal gaps | Missing positions at 3' ende | Percent coveragef |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1003 | 3.33 | 546797 | 540519 | 2|37|38|38|38 | 2|36|37|38|38 | NDV | 0|4229|6090|8762|18055 | 525597 | 15127 | 65 | 99.57 | ||
| IBV g | 0|2|5|8|44 | 904 | 23711 | 269 | 3644 | 18 | 85.78 | ||||||
| 1005 | 3.44 | 564101 | 123024 | 2|36|37|38|38 | 2|33|36|37|38 | NDV h | 0|7|13|19|36 | 1161 | 14494 | 343 | 272 | 83 | 95.41 |
| AIV i - PB2 | 2|685|1003|1446|2774 | 16804 | 2283 | 100.00 | |||||||||
| AIV - PB1 | 2|1845|2896|3432|4634 | 38261 | 2334 | 100.00 | |||||||||
| AIV - PA | 68|1180|1496|1970|4721 | 23466 | 2151 | 100.00 | |||||||||
| AIV - HA | 12|595|1057|1598|2604 | 14687 | 1683 | 100.00 | |||||||||
| AIV - NP | 25|886|1306|1867|2563 | 11252 | 1497 | 100.00 | |||||||||
| AIV - NA | 11|416|838|1030|1692 | 7707 | 1410 | 100.00 | |||||||||
| AIV - M1, M2 | 11|210|811|1357|2195 | 5699 | 982 | 100.00 | |||||||||
| AIV - NEP, NS1 | 15|396|787|1222|1707 | 3796 | 838 | 100.00 | |||||||||
| 1009 | 3.21 | 526425 | 519854 | 2|37|38|38|38 | 2|36|37|38|38 | NDV | 0|4216|6887|9403|18079 | 485669 | 15127 | 65 | 99.57 | ||
| IBV | 0|15|22|35|92 | 3743 | 27469 | 136 | 19 | 18 | 99.37 | ||||||
| AIV - PB2 | 0|137|175|272|545 | 2791 | 2283 | 100.00 | |||||||||
| AIV - PB1 | 3|370|651|835|1177 | 7692 | 2324 | 20 | 98.99 | ||||||||
| AIV - PA | 0|88|117|183|446 | 1675 | 2151 | 100.00 | |||||||||
| AIV - HA | 0|113|256|342|578 | 2399 | 1683 | 100.00 | |||||||||
| AIV - NP | 0|145|277|333|523 | 2117 | 1485 | 100.00 | |||||||||
| AIV - NA | 4|118|225|317|637 | 2226 | 1410 | 100.00 | |||||||||
| AIV - M1,M2 | 2|46|132|183|246 | 793 | 958 | 24 | 96.71 | ||||||||
| AIV - NEP, NS1 | 0|47|83|103|139 | 368 | 838 | 100.00 | |||||||||
| 1011 | 3.44 | 565083 | 538171 | 2|37|38|38|38 | 2|36|37|38|38 | NDV | 1|3272|5386|7121|16101 | 499378 | 15192 | 100.00 | |||
| AIV - PB2 | 0|181|290|462|1254 | 6242 | 2283 | 100.00 | |||||||||
| AIV - PB1 | 2|323|482|609|1077 | 7728 | 2334 | 100.00 | |||||||||
| AIV - PA | 8|127|172|220|437 | 2743 | 2151 | 100.00 | |||||||||
| AIV - HA | 3|217|449|685|906 | 5306 | 1683 | 100.00 | |||||||||
| AIV - NP | 3|180|380|605|758 | 4314 | 1497 | 100.00 | |||||||||
| AIV - NA | 3|74|98|153|242 | 1383 | 1410 | 100.00 | |||||||||
| AIV - M1,M2 | 4|59|255|372|579 | 2092 | 982 | 100.00 | |||||||||
| AIV - NEP, NS1 | 3|29|70|137|216 | 516 | 808 | 100.00 | |||||||||
| 998 | 1.80 | 295662 | 294217 | 2|37|38|38|38 | 2|35|37|38|38 | NDV | 0|2248|3275|4719|11528 | 280492 | 15103 | 20 | 69 | 99.41 | |
| AIV - PB2 | 0|22|33|48|78 | 477 | 2246 | 34 | 98.51 | ||||||||
| AIV - PB1 | 0|34|56|85|125 | 698 | 2217 | 60 | 97.36 | ||||||||
| AIV - PA | 2|28|55|106|178 | 767 | 2141 | 10 | 99.53 | ||||||||
| AIV - HA | 0|9|18|29|53 | 204 | 1643 | 40 | 97.65 | ||||||||
| AIV - NP | 0|24|43|82|126 | 430 | 1456 | 35 | 6 | 97.26 | |||||||
| AIV - NA | 1|21|28|41|83 | 272 | 1304 | 31 | 75 | 92.23 | |||||||
| AIV - M1,M2 | 0|8|28|65|87 | 196 | 923 | 56 | 92.62 | ||||||||
| AIV - NEP, NS1 | 0|9|17|28|40 | 94 | 810 | 100.00 |
a the fraction of reads assigned to each sample out of all number of reads that passed filter (i.e. pass-filter reads)
b the number of paired reads remaining after host and internal control filtering
c numbers represent distribution (minimum | lower quartile | median | upper quartile | maximum)
d numbers of paired reads used to re-call the final consensus for each sequence
e for avian influenza viruses, the missing nucleotides refer to the beginning and the end of the coding sequences of the genes
f the fraction of the expected full genome length covered by the consensus scaffold (i.e. not containing unknown nucleotides), for avian influenza genes, the coverage represents comparison to the coding sequences of the genes only
g Infectious bronchitis virus
h coverage depth and number of reads used to re-call the final consensus for this NDV isolate were impacted by the presence of influenza virus A in the sample (influenza reads were estimated to be approximately 98% of all reads, data not shown)
i Avian influenza virus; PB2 = segment 1 polymerase PB2; PB1 = segment 2 polymerase PB1; PA = segment 3 polymerase PA; HA = segment 4 hemagglutinin; NP = segment 5 nucleocapsid protein; NA = segment 6 neuraminidase; M1, M2 = segment 7 matrix protein 1 and matrix protein 2; NEP = segment 8 nuclear export protein and nonstructural protein 1