Table 3 Total number of SNVs detected using Platypus compared to simple filtering
From: Identification of pathogen genomic variants through an integrated pipeline
Experiment ID | # Raw SNVs | # SNVs from Q30 | # SNVs from Platypus | Amino acid change conferring resistance | Genome total-fold coverage |
|---|---|---|---|---|---|
KAD707B1 | 613972 | 20 | 12 | L830V, M1069I | 43x |
KAD707B2 | 50145 | 10 | 6 | M81I, L830V | 62x |
KAD707B3 | 52389 | 5 | 3 | L830V, S1076I | 50x |
KAD458 | 60250 | 13 | 8 | S1076I, V1053A | 25x |
CladoR_clone1 | 82488 | 53 | 32 | n/a (CNV) | 67x |
CladoR_clone2 | 100033 | 80 | 48 | n/a (CNV) | 42x |
CladoR_clone3 | 107611 | 68 | 41 | n/a (CNV) | 47x |
NITD609_1 | 50008 | 8 | 5 | I398F, P990R, CNV | 49x |
NITD609_2 | 48201 | 12 | 7 | T418N, P990R | 48x |
NITD609_3 | 48484 | 13 | 8 | D1247Y | 36x |
NITD678_1 | 51665 | 18 | 11 | G223R | 39x |
NITD678_2 | 56756 | 15 | 9 | A184S, P990R | 42x |
NITD678_3 | 83190 | 55 | 33 | I203M, I263V | 44x |
EvoR1a | 45388 | 8 | 5 | M133V | 83x |
EvoR1a2 | 46151 | 12 | 7 | M133V | 76x |
EvoR1b | 46462 | 10 | 6 | M133V | 60x |
EvoR1b2 | 46377 | 15 | 9 | M133V | 79x |
EvoR2a | 45565 | 3 | 2 | M133I | 64x |
EvoR2a2 | 45604 | 3 | 2 | M133I | 67x |
EvoR2b* | n/a* | n/a* | n/a* | n/a* | 1x |
EvoR2b2 | 38188 | 3 | 2 | M133I | 82x |
EvoR3a | 38224 | 7 | 4 | M133I | 54x |
EvoR3b | 38620 | 7 | 4 | M133I | 62x |
EvoR4a | 37404 | 5 | 3 | M133I, L144S | 67x |
EvoR4b | 38333 | 5 | 3 | M133I, L144S | 78x |
EvoR5a | 46563 | 3 | 2 | F267V | 79x |
EvoR5b | 46890 | 3 | 2 | F267V | 65x |