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 | Â | 65 | Â | 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 | Â | Â | Â | 100.00 | ||||||
AIV - PB1 | 2|1845|2896|3432|4634 | 38261 | 2334 | Â | Â | Â | 100.00 | ||||||
AIV - PA | 68|1180|1496|1970|4721 | 23466 | 2151 | Â | Â | Â | 100.00 | ||||||
AIV - HA | 12|595|1057|1598|2604 | 14687 | 1683 | Â | Â | Â | 100.00 | ||||||
AIV - NP | 25|886|1306|1867|2563 | 11252 | 1497 | Â | Â | Â | 100.00 | ||||||
AIV - NA | 11|416|838|1030|1692 | 7707 | 1410 | Â | Â | Â | 100.00 | ||||||
AIV - M1, M2 | 11|210|811|1357|2195 | 5699 | 982 | Â | Â | Â | 100.00 | ||||||
AIV - NEP, NS1 | 15|396|787|1222|1707 | 3796 | 838 | Â | Â | Â | 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 | Â | 65 | Â | 99.57 |
IBV | 0|15|22|35|92 | 3743 | 27469 | 136 | 19 | 18 | 99.37 | ||||||
AIV - PB2 | 0|137|175|272|545 | 2791 | 2283 | Â | Â | Â | 100.00 | ||||||
AIV - PB1 | 3|370|651|835|1177 | 7692 | 2324 | 20 | Â | Â | 98.99 | ||||||
AIV - PA | 0|88|117|183|446 | 1675 | 2151 | Â | Â | Â | 100.00 | ||||||
AIV - HA | 0|113|256|342|578 | 2399 | 1683 | Â | Â | Â | 100.00 | ||||||
AIV - NP | 0|145|277|333|523 | 2117 | 1485 | Â | Â | Â | 100.00 | ||||||
AIV - NA | 4|118|225|317|637 | 2226 | 1410 | Â | Â | Â | 100.00 | ||||||
AIV - M1,M2 | 2|46|132|183|246 | 793 | 958 | 24 | Â | Â | 96.71 | ||||||
AIV - NEP, NS1 | 0|47|83|103|139 | 368 | 838 | Â | Â | Â | 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 | Â | Â | Â | 100.00 |
AIV - PB2 | 0|181|290|462|1254 | 6242 | 2283 | Â | Â | Â | 100.00 | ||||||
AIV - PB1 | 2|323|482|609|1077 | 7728 | 2334 | Â | Â | Â | 100.00 | ||||||
AIV - PA | 8|127|172|220|437 | 2743 | 2151 | Â | Â | Â | 100.00 | ||||||
AIV - HA | 3|217|449|685|906 | 5306 | 1683 | Â | Â | Â | 100.00 | ||||||
AIV - NP | 3|180|380|605|758 | 4314 | 1497 | Â | Â | Â | 100.00 | ||||||
AIV - NA | 3|74|98|153|242 | 1383 | 1410 | Â | Â | Â | 100.00 | ||||||
AIV - M1,M2 | 4|59|255|372|579 | 2092 | 982 | Â | Â | Â | 100.00 | ||||||
AIV - NEP, NS1 | 3|29|70|137|216 | 516 | 808 | Â | Â | Â | 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 | Â | 99.41 |
AIV - PB2 | 0|22|33|48|78 | 477 | 2246 | Â | Â | 34 | 98.51 | ||||||
AIV - PB1 | 0|34|56|85|125 | 698 | 2217 | Â | Â | 60 | 97.36 | ||||||
AIV - PA | 2|28|55|106|178 | 767 | 2141 | 10 | Â | Â | 99.53 | ||||||
AIV - HA | 0|9|18|29|53 | 204 | 1643 | Â | Â | 40 | 97.65 | ||||||
AIV - NP | 0|24|43|82|126 | 430 | 1456 | 35 | Â | 6 | 97.26 | ||||||
AIV - NA | 1|21|28|41|83 | 272 | 1304 | 31 | Â | 75 | 92.23 | ||||||
AIV - M1,M2 | 0|8|28|65|87 | 196 | 923 | 56 | Â | Â | 92.62 | ||||||
AIV - NEP, NS1 | 0|9|17|28|40 | 94 | 810 | Â | Â | Â | 100.00 |