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. 2020 Feb 20;15(2):e0229326. doi: 10.1371/journal.pone.0229326

Table 5. The reproducibility of positions with at least one ≥5% variant when alignment files from the respective DPPs are all uploaded into DPP3 for only the mSNV identification process versus when the mSNV identifications are fully performed by the respective DPPs.

Virus Position Sequence platform Data Processing pipeline Bam file generating processing pipeline
1 2 3 1 2 3
Minor variants Percentage Minor variants Percentage Minor variants Percentage Minor variants Percentage Minor variants Percentage Minor variants Percentage
NLCH PB2.1879 G→A 1 81/1301 6,2% 246/2716 9,1% 112/1203 9,3% 132/1375 9,6% 246/2716 9,1% 121/1301 9,3%
2 47/956 4,9% 117/1137 10,3% 114/1064 10,7% 119/1122 10,6% 117/1137 10,3% 114/1064 10,7%
3 49/530 9,2% 131/1341 9,8% 129/1338 9,6% 54/542 10,0% 131//1341 9,8% 129/1338 9,6%
PB2.2101 G→A 1 53/1118 4,7% 261/2704 9,7% 110/897 12,3% 138/1180 11,7% 261/2704 9,7% 121/1086 11,1%
2 21/1578 1,3% 125/1875 6,7% 121/1463 8,3% ND/1856## <1% ND/1850# <1% 121/1463 8,3%
3 13/542 2,4% 199/1433 13,9% 199/1435 13,9% 87/625 13,9% 199/1433 13,9% 199/1435 13,9%
PB2.2277 T→G 1 ND/479 <1% 86/1008 8,5% 33/190 17,4% ND/849 <1% ND/1008## <1% 37/281 13,2%
2 ND/557 <1% ND/623 <1% ND/534 <1% ND/619 <1% ND/623 <1% ND/534 <1%
3 ND/680 <1% ND/1117 <1% ND/1024 <1% ND/708 <1% ND/1117 <1% ND/1027 <1%
PB1.87 A→G 1 ND/818 <1% ND/1754 <1% ND/1114 <1% ND/1264 <1% ND/1753 <1% ND/1114 <1%
2 25/230 10,9% ND/376 <1% ND/328 <1% ND/368## <1% ND/376 <1% ND/328 <1%
3 ND/275 <1% ND/537 <1% ND/537 <1% ND/278 <1% ND/537 <1% ND/537 <1%
PB1.2240 G→C 1 ND/664 <1% 54/1341 4,0% 38/418 9,1% ND/1004 <1% ND/1341# <1% 46/486 9,5%
2 ND/1231 <1% ND/1271 <1% ND/1233 <1% ND/1277 <1% ND/1271 <1% ND/1235 <1%
3 ND/161 <1% ND/277 <1% ND/276 <1% ND/163 <1% ND/277 <1% ND/276 <1%
PB1.2268 A→G 1 ND/336 <1% 29/641 4,5% 11/176 6,3% 15/322* 4,66%* 37/641 5,8% 13/213 6,1%
2 ND/993 <1% ND/1026 <1% ND/1002 <1% ND/1025 <1% ND/1026 <1% ND/1002 <1%
3 ND/53 <1% ND/159 <1% ND/148 <1% ND/90 <1% ND/159 <1% ND/151 <1%
PA.2167 T→G 1 ND/141 <1% ND/288 <1% ND/154 <1% ND/235 <1% 21/288* 7,29%* ND/154 <1%
2 ND/757 <1% ND/807 <1% ND/773 <1% ND/812 <1% ND/807 <1% ND/733 <1%
3 ND/704 <1% ND/1070 <1% ND/1077 <1% ND/714 <1% ND/1070 <1% ND/1078 <1%
HA.104 A→G 1 ND/733 <1% ND/1761 <1% ND/1151 <1% ND/1175 <1% ND/1761 <1% ND/1135 <1%
2 ND/437 <1% ND/1370 <1% ND/1156 <1% ND/1326 <1% ND/1369 <1% ND/1142 <1%
3 ND/1 <1% ND/105 <1% 12/105 11,4% ND/6 <1% ND/105 <1% 12/105 11,4%
HA.1689 T→C 1 ND/390 <1% ND/694 <1% 11/217 5,1% ND/610 <1% ND/694 <1% 13/260 5,0%
2 ND/2018 <1% ND/4083 <1% ND/3979 <1% ND/4045 <1% ND/4081 <1% ND/3979 <1%
3 ND/937 <1% ND/1669 <1% ND/1680 <1% ND/1106 <1% ND/1669 <1% ND/1680 <1%
NA.3 T→C 1 ND/32 <1% ND/105 <1% ND/49 <1% ND/92 <1% 7/105* 6,67%* ND/49 <1%
2 ND/6 <1% ND/313 <1% ND/297 <1% ND/305 <1% ND/313 <1% ND/297 <1%
3 ND/2 <1% ND/25 <1% ND/25 <1% ND/6 <1% ND/25 <1% ND/25 <1%
NP.105 A→G 1 ND/182 <1% ND/449 <1% ND/343 <1% ND/374 <1% 6/449* 1,34%* ND/343 <1%
2 83/1507 5,5% ND/1890 <1% ND/1804 <1% ND/1866## <1% ND/1890 <1% ND/1805 <1%
3 ND/89 <1% ND/704 <1% ND/702 <1% ND/246 <1% ND/704 <1% ND/703 <1%
NP.1239 A→T 1 32/2428 1,3% 279/5410 5,2% ND/3092 <1% ND/3372## <1% ND/5410# <1% ND/3092 <1%
2 ND/2345 <1% ND/2643 <1% ND/2453 <1% ND/2626 <1% ND/2643 <1% ND/2453 <1%
3 ND/1711 <1% ND/2111 <1% ND/2117 <1% ND/1712 <1% ND/2111 <1% ND/2117 <1%
NP.1489 G→A 1 ND/182 <1% 26/336 7,7% ND/172 <1% ND/242 <1% 26/376* 6,9% ND/172 <1%
2 ND/436 <1% ND/452 <1% ND/444 <1% ND/451 <1% ND/451 <1% ND/444 <1%
3 ND/1320 <1% ND/1799 <1% ND/1799 <1% ND/1325 <1% ND/1799 <1% ND/1799 <1%
NS.827 C→T 1 ND/249 <1% 19/419 4,5% ND/205 <1% ND/365 <1% 21/412 5,3% ND/205 <1%
2 ND/1316 <1% ND/1423 <1% ND/1375 <1% ND/1427 <1% ND/1422 <1% ND/1375 <1%
3 ND/2091 <1% ND/2901 <1% ND/2757 <1% ND/2293 <1% ND/2898 <1% ND/2929 <1%
NS829 G→T 1 ND/221 <1% 19/380 5,0% ND/179 <1% ND/328 <1% 19/376 5,4% ND/179 <1%
2 ND/1302 <1% ND/1391 <1% ND/1341 <1% ND/1388 <1% ND/1389 <1% ND/1341 <1%
3 ND/2117 <1% ND/2852 <1% ND/2727 <1% ND/2279 <1% ND/2852 <1% ND/2880 <1%
NS.833 A→T 1 ND/187 <1% ND/287 <1% 5/88 5,7% ND/259 <1% 11/257* 4,28%* 5/96 5,2%
2 ND/1224 <1% ND/1327 <1% ND/1284 <1% ND/1314 <1% ND/1322 <1% ND/1284 <1%
3 ND/1367 <1% ND/2430 <1% ND/2333 <1% ND/1779 <1% ND/2430 <1% ND/2360 <1%
DETU PB2.900 A→G 1 38/1335 2,9% 136/2740 5,0% 61/1231 5,0% 68/1328 5,12 136/2740 4,96 65/1322 4,92
2 35/1645 2,1% 77/1800 4,3% 66/1629 4,1% 70/1775 4,0% 77/1800 4,3% 66/1629 4,1%
3 30/861 3,5% 86/2308 3,7% 47/1245 3,8% ND/1001## <1% ND/2308# <1% 47/1245 3,8%
PB2.1054 T→C 1 69/1369 5,0% 168/2637 6,4% 97/1304 7,4% 105/1393 7,5% 168/2637 6,4% 100/1376 7,3%
2 60/1477 4,1% 115/1836 6,3% 99/1605 6,2% 113/1810 6,2% 115/1836 6,3% 99/1605 6,2%
3 6/392 1,5% 94/2038 4,6% 48/1054 4,6% 32/524 6,1% 94/2038 4,6% 48/1054 4,6%
PB2.2257 A→C 1 ND/867 <1% ND/1563 <1% 24/463 5,2% ND/1447 <1% ND/1562 <1% 26/472 5,5%
2 ND/531 <1% ND/581 <1% ND/378 <1% ND/588 <1% ND/580 <1% ND/378 <1%
3 ND/893 <1% ND/2286 <1% ND/1346 <1% ND/1341 <1% ND/2185 <1% ND/1347 <1%
PB2.2277 T→G 1 ND/644 <1% 52/1150 4,5% 27/307 8,8% ND/1062 <1% ND/1150# <1% 28/381 7,4%
2 ND/418 <1% ND/472 <1% ND/284 <1% ND/474 <1% ND/472 <1% ND/284 <1%
3 ND/1208 <1% ND/1948 <1% ND/1209 <1% ND/1251 <1% ND/1948 <1% ND/1214 <1%
PB1.14 C→T 1 ND/144 <1% 48/433 11,1% ND/239 <1% ND/362 <1% 48/433 11,1% ND/239 <1%
2 ND/90 <1% ND/355 <1% ND/304 <1% ND/345 <1% ND/351 <1% ND/304 <1%
3 ND/562 <1% ND/792 <1% ND/496 <1% ND/633 <1% ND/655 <1% ND/504 <1%
PB1.23 T→G 1 ND/207 <1% 30/535 5,6% ND/315 <1% ND/470 <1% 30/535 5,6% ND/315 <1%
2 ND/103 <1% ND/365 <1% ND/319 <1% ND/365 <1% 4/365* 1,96%* ND/319 <1%
3 ND/699 <1% ND/950 <1% ND/609 <1% ND/702 <1% ND/950 <1% ND/609 <1%
PB1.87 A→G 1 ND/744 <1% ND/1644 <1% ND/1076 <1% ND/1218 <1% ND/1644 <1% ND/1076 <1%
2 49/365 13,4% ND/677 <1% ND/576 <1% 13/638 2,0% ND/674 <1% ND/576 <1%
3 ND/721 <1% ND/1156 <1% ND/793 <1% ND/731 <1% ND/1156 <1% ND/793 <1%
PB1.2240 G→C 1 ND/757 <1% 23/1517 1,5% 26/515 5,0% ND/1266 <1% ND/1515# <1% 28/631 4,4%
2 ND/944 <1% ND/985 <1% ND/806 <1% ND/994 <1% ND/984 <1% ND/806 <1%
3 ND/274 <1% ND/439 <1% ND/253 <1% ND/301 <1% ND/439 <1% ND/253 <1%
PB1.2268 A→G 1 5/470 1,1% 33/928 3,6% 22/278 7,9% 28/420 6,7% ND/928## <1% 23/354 6,5%
2 ND/798 <1% ND/829 <1% ND/671 <1% ND/839 <1% ND/829 <1% ND/671 <1%
3 ND/109 <1% ND/259 <1% ND/123 <1% ND/193 <1% ND/259 <1% ND/126 <1%
PB1.2271 A→G 1 12/446 2,7% 59/901 6,5% 16/263 6,1% 29/413 7,0% 59/901 6,6% 21/336 6,3%
2 ND/729 <1% 47/810 5,8% 40/649 6,2% 43/750* 5,73%* 47/810 5,8% 40/649 6,2%
3 1/32 3,1% ND/123 <1% 2/83 2,4% 5/75 6,7% 5/124* 4,03%* 2/83 2,4%
HA.867 C→T 1 59/1533 3,8% 206/3183 6,5% 104/1537 6,8% 112/1584 7,1% 206/3183 6,5% 109/1573 6,9%
2 59/2031 2,9% 150/2525 5,9% 127/2253 5,6% 144/2502 5,8% 150/2525 5,9% 127/2253 5,6%
3 11/180 6,1% 48/647 7,4% 28/385 7,3% 13/182 7,1% 48/647 7,4% 28/385 7,3%
HA.963 T→C 1 122/1401 8,7% 446/3071 14,5% 189/1419 13,3% 200/1468 13,6% 446/3071 14,5% 193/1455 13,3%
2 90/1517 5,9% 318/2189 14,5% 247/1828 13,5% 308/2165 14,2% 318/2189 14,5% 247/1828 13,5%
3 5/69 7,2% 107/606 17,7% 47/293 16,0% 12/81 14,8% 107/606 17,7% 47/293 16,0%
NP.1491 C→A 1 ND/278 <1% 71/583 12,2% ND/206 <1% ND/390 <1% ND/579# <1% ND/206 <1%
2 ND/723 <1% ND/769 <1% ND/692 <1% ND/766 <1% ND/769 <1% ND/692 <1%
3 ND/799 <1% ND/2031 <1% ND/1206 <1% ND/858 <1% ND/2031 <1% ND/1206 <1%
NA.65 T→C 1 19/503 3,8% 52/1229 4,2% 16/467 3,4% 22/535 4,1% 52/1229 4,2% 20/540 3,7%
2 20/662 3,0% 50/1104 4,5% 45/992 4,5% 52/1063 4,9% 50/1104 4,5% 45/992 4,5%
3 24/557 4,3% 53/1099 4,8% 37/727 5,1% 28/584 4,8% 53/1099 4,8% 37/727 5,1%
NA.78 T→C 1 23/599 3,8% 57/1403 4,1% 20/557 3,6% 23/622 3,7% 57/1403 4,1% 24/638 3,8%
2 21/692 3,0% 55/1147 4,8% 50/1033 4,8% 54/1109 4,9% 55/1147 4,8% 50/1033 4,8%
3 23/580 4,0% 51/1124 4,5% 37/735 5,0% 27/585 4,6% ND/1124# <1% 37/735 5,0%
NA.89 T→C 1 23/713 3,2% 55/1670 3,3% 22/651 3,4% 26/731 3,6% 55/1670 3,3% 26/751 3,5%
2 23/798 2,9% 56/1261 4,4% 50/1134 4,4% 54/1224 4,4% 56/1261 4,4% 50/1134 4,4%
3 24/580 4,1% 55/1196 4,6% 40/775 5,2% 28/587 4,8% 55/1196 4,6% 40/775 5,2%
NA.117 T→C 1 37/908 4,1% 87/2140 4,1% 36/818 4,4% 40/914 4,4% 87/2140 4,7% 43/922 4,7%
2 28/1102 2,5% 67/1631 4,1% ND/1459 <1% 70/1586 4,4% 67/1631 4,1% ND/1459 <1%
3 22/531 4,1% 57/1276 4,5% 42/812 5,2% 28/544 5,2% ND/1276# <1% 42/812 5,2%
NA.126 T→C 1 37/983 3,8% 83/2294 3,6% 36/876 4,1% 39/973 4,0% 83/2294 3,6% 43/981 4,4%
2 31/1126 2,8% 72/1676 4,3% 65/1502 4,3% 75/1616 4,6% 72/1676 4,3% 65/1502 4,3%
3 26/519 5,0% 62/1395 4,4% 43/812 5,3% 30/537 5,6% 62/1395 4,4% 43/812 5,3%
UKDD PB2.2277 T→G 1 ND/415 <1% 28/507 5,5% ND/475 <1% ND/503 <1% ND/507# <1% ND/475 <1%
2 ND/589 <1% ND/620 <1% ND/601 <1% ND/627 <1% ND/620 <1% ND/601 <1%
3 ND/1140 <1% ND/1996 <1% ND/2065 <1% ND/1186 <1% ND/1996 <1% ND/2071 <1%
PB2.2278 T→G 1 ND/367 <1% ND/471 <1% ND/464## <1% ND/465 <1% ND/471 <1% 17/268 6,3%
2 ND/581 <1% ND/613 <1% ND/581 <1% ND/621 <1% ND/588 <1% ND/581 <1%
3 ND/1141 <1% ND/1985 <1% ND/1993 <1% ND/1184 <1% ND/1975 <1% ND/2004 <1%
PB1.87 A→G 1 ND/387 <1% ND/440 <1% ND/439 <1% ND/451 <1% ND/417 <1% ND/439 <1%
2 26/327 8,0% 32/395 8,1% ND/351 <1% 33/385 8,6% ND/395# <1% ND/351 <1%
3 ND/617 <1% ND/1133 <1% ND/1136 <1% ND/622 <1% ND/1133 <1% ND/1136 <1%
PB1.728 C→A 1 ND/750 <1% ND/832 <1% ND/836 <1% ND/853 <1% ND/832 <1% ND/836 <1%
2 ND/776 <1% 52/928 5,6% ND/829 <1% ND/888 <1% ND/912## <1% ND/829 <1%
3 ND/2459 <1% ND/4290 <1% ND/4293 <1% ND/2471 <1% ND/4287 <1% ND/4292 <1%
PB1.730 C→T 1 ND/742 <1% ND/824 <1% ND/826 <1% ND/844 <1% ND/824 <1% ND/826 <1%
2 ND/767 <1% 57/1008 5,7% ND/832 <1% ND/893 <1% ND/1008# <1% ND/832 <1%
3 ND/2339 <1% ND//4286 <1% ND/4289 <1% ND/2464 <1% ND/4285 <1% ND/4284 <1%
PB1.883 G→C 1 ND/942 <1% ND/997 <1% ND/997 <1% ND/1016 <1% ND/997 <1% ND/997 <1%
2 ND/1689 <1% ND/1856 <1% ND/1760 <1% ND/1867 <1% ND/1856 <1% ND/1760 <1%
3 ND/2479 <1% 47/690 6,8% ND/3681 <1% ND/2635 <1% ND/690## <1% ND/3697 <1%
PA.49 G→C 1 ND/103 <1% 6/117 5,1% ND/115 <1% ND/113 <1% ND/117# <1% ND/115 <1%
2 ND/337 <1% ND/435 <1% ND/392 <1% ND/441 <1% ND/434 <1% ND/392 <1%
3 ND/111 <1% ND/207 <1% ND/204 <1% ND/113 <1% ND/206 <1% ND/206 <1%
PA.82 C→T 1 ND/155 <1% ND/180 <1% ND/177 <1% ND/179 <1% ND/180 <1% ND/177 <1%
2 ND/695 <1% ND/809 <1% ND/745 <1% ND/797 <1% ND/809 <1% ND/745 <1%
3 ND/64 <1% ND/247 <1% 30/248 12,1% ND/74 <1% ND/247 <1% 30/248 12,1%
NS.811 G→T 1 ND/221 <1% 17/270 6,3% ND/249 <1% ND/261 <1% ND/270# <1% ND/249 <1%
2 ND/2452 <1% ND/2725 <1% ND/2557 <1% ND/2742 <1% ND/2725 <1% ND/2557 <1%
3 ND/3117 <1% ND/4125 <1% ND/4139 <1% ND/3188 <1% ND/4124 <1% ND/4142 <1%

*Locations containing mSNV detections in the DPP3 mSNV analysis of the bam files but not in the original DPPs; Locations containing ≥1% mSNVs that could be reproduced by deleting DPP3s default ‘Direction and position filters’ with those exactly reproduced (#) and those approximately reproduced but with different coverages and/or variants (##).