Skip to main content

Advertisement

Table 2 Summary of sequencing and assembly data of 25 avian paramyxovirus isolates

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 coveragee
1002 2.49 409193 405137 2|37|38|38|38 2|36|37|38|38 NDV 0|3680|6088|7868|18004 390740 15124   68   99.55
1004 2.67 437755 432361 2|37|38|38|38 2|34|37|38|38 NDV 0|4185|6151|7909|14329 422150 15125   67   99.56
1007 4.20 688524 681691 2|37|38|38|38 2|36|37|38|38 NDV 0|817|3648|7368|19348 665220 15125   67   99.56
994 1.39 227500 226196 2|37|38|38|38 2|36|37|38|38 NDV 0|1758|2756|4186|14276 219609 15121   71   99.53
995 1.38 226050 224416 2|36|37|38|38 2|34|36|37|38 NDV 0|2162|2995|4197|9101 216240 15110   82   99.46
996 1.53 251238 250338 2|37|38|38|38 2|34|37|37|38 NDV 0|2383|3175|4411|9167 242158 15104 20 68   99.42
1001 3.79 621655 618002 2|37|38|38|38 2|36|37|38|38 NDV 0|4653|6784|9510|21623 594361 15122   70   99.54
997 1.72 281376 266251 2|37|38|38|38 2|35|37|38|38 NDV 0|1937|3026|4030|9645 233775 15104 22 66   99.42
999 1.70 279207 272105 2|37|38|38|38 2|36|37|38|38 NDV 0|1728|2583|4496|11915 241105 15108   84   99.45
1000 1.74 285079 280596 2|37|38|38|38 2|35|37|38|38 NDV 0|2338|3107|4441|8796 241724 15117   75   99.51
959 3.60 590494 588212 2|37|38|38|38 2|37|38|38|38 APMV-13 1|2250|3484|5801|23998 531520 16126 20    99.88
960 4.34 711909 709377 2|37|37|38|38 2|37|37|38|38 NDV 0|3738|5631|7347|19491 628837 15135 25 32   99.62
961 4.61 756197 753487 2|36|37|38|38 2|35|37|38|38 NDV 0|4585|6509|8206|14939 674667 15167 25    99.84
962 3.35 548833 547622 2|37|38|38|38 2|35|37|38|38 NDV 2|4617|6340|8772|14719 529553 15192     100.00
967 3.71 607876 597902 2|37|38|38|38 2|36|37|38|38 NDV 2|2673|3928|6881|26072 562657 15192     100.00
968 4.46 731692 727838 2|37|38|38|38 2|35|37|38|38 NDV 0|2507|4136|7393|22877 636218 15167 19    99.87
695 7.16 1156516 1129415 2|36|37|38|38 2|35|37|38|38 NDV 2|1678|3827|6301|32862 955829 15192     100.00
714 3.98 653603 643246 2|37|37|38|38 2|36|37|38|38 NDV 1|2082|3513|6724|35052 570825 15192     100.00
715 3.63 594802 580223 2|37|38|38|38 2|36|37|38|38 NDV 10|2608|5633|8881|28809 526885 15192     100.00
720 4.05 663757 657982 2|37|37|38|38 2|35|37|38|38 NDV 13|3821|6267|9252|27439 525313 15192     100.00
861 3.51 576077 574864 2|37|38|38|38 2|35|37|38|38 NDV 6|3930|6419|8881|27153 559394 15192     100.00
867 4.11 673510 668781 2|37|38|38|38 2|36|37|38|38 NDV 0|4284|6079|9028|23441 647586 15176 16    99.89
892 3.92 642753 642250 2|37|38|38|38 2|35|37|38|38 NDV 1|5147|7049|9922|18221 618591 15180 12    99.92
913 4.06 665640 661350 2|36|37|38|38 2|35|37|38|38 NDV 0|2278|3784|7011|31842 566280 15192     100.00
688 0.01 no data NA NA NA NA NA   NA NA NA NA NA
  1. NA not applicable
  2. a the fraction of reads assigned to each sample out of all number of reads that passed filter (i.e. pass-filter reads)
  3. b the number of paired reads remaining after host and internal control filtering
  4. c numbers represent distribution (minimum | lower quartile | median | upper quartile | maximum)
  5. d numbers of paired reads used to re-call the final consensus for each sequence
  6. e the missing nucleotides at the ends and the fraction of the expected full genome length covered by the consensus scaffold (i.e. not containing unknown nucleotides)