Table 2.
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 |
NA not applicable
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 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)