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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

From: A robust and cost-effective approach to sequence and analyze complete genomes of small RNA 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
  1. a the fraction of reads assigned to each sample out of all number of reads that passed filter (i.e. pass-filter reads)
  2. b the number of paired reads remaining after host and internal control filtering
  3. c numbers represent distribution (minimum | lower quartile | median | upper quartile | maximum)
  4. d numbers of paired reads used to re-call the final consensus for each sequence
  5. e for avian influenza viruses, the missing nucleotides refer to the beginning and the end of the coding sequences of the genes
  6. 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
  7. g Infectious bronchitis virus
  8. 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)
  9. 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