Automated quality control for a molecular surveillance system

Sims, Seth; Longmire, Atkinson G.; Campo, David S.; Ramachandran, Sumathi; Medrzycki, Magdalena; Ganova-Raeva, Lilia; Lin, Yulin; Sue, Amanda; Thai, Hong; Zelikovsky, Alexander; Khudyakov, Yury

doi:10.1186/s12859-018-2329-5

BMC Bioinformatics

Table 3 Welch’s test for mean comparison of means

From: Automated quality control for a molecular surveillance system

Comparison	Filter	t	p-value	Corrected p-value	Reject
P vs F	Primer dimer	2.485304	3.220E-02	7.210E-01	FALSE
P vs F	Ambiguity	−2.64516	8.258E-03	2.999E-01	FALSE
P vs F	Short read	1.227051	2.478E-01	9.995E-01	FALSE
P vs F	MID mismatch	1.721249	1.159E-01	9.828E-01	FALSE
P vs F	Minority MID	1.491232	1.666E-01	9.949E-01	FALSE
P vs F	Primer verification	0.318833	7.561E-01	1.000E + 00	FALSE
P vs F	Casper mismatch	2.09018	6.284E-02	9.033E-01	FALSE
P vs F	Nonsense	0.600825	5.611E-01	1.000E + 00	FALSE
P vs F	raw pairs passed	−1.65813	1.279E-01	9.875E-01	FALSE
P vs F	r1_maxlength	0.027582	9.785E-01	1.000E + 00	FALSE
P vs F	r2_maxlength	0.027582	9.785E-01	1.000E + 00	FALSE
P vs F	r1_numseqs	0.496099	6.303E-01	1.000E + 00	FALSE
P vs F	r2_numseqs	0.496099	6.303E-01	1.000E + 00	FALSE
P vs F	r1_minlength	−2.61235	2.243E-02	6.055E-01	FALSE
P vs F	r2_minlength	−1.40858	1.889E-01	9.972E-01	FALSE
P vs F	r1_gc	0.9154	3.810E-01	1.000E + 00	FALSE
P vs F	r2_gc	1.115745	2.897E-01	9.999E-01	FALSE
P vs F	r1_qual	−0.7403	4.759E-01	1.000E + 00	FALSE
P vs F	r2_qual	−0.22578	8.259E-01	1.000E + 00	FALSE
PN vs PNN	Primer dimer	−20.708	2.919E-67	0.000E + 00	TRUE
PN vs PNN	Ambiguity	−3.81125	1.589E-04	7.125E-03	TRUE
PN vs PNN	Short read	−9.98183	3.000E-21	0.000E + 00	TRUE
PN vs PNN	MID mismatch	−20.5454	1.447E-66	0.000E + 00	TRUE
PN vs PNN	Minority MID	−18.9948	1.667E-58	0.000E + 00	TRUE
PN vs PNN	Primer verification	−6.14462	1.853E-09	9.082E-08	TRUE
PN vs PNN	Casper mismatch	−14.2144	3.668E-39	0.000E + 00	TRUE
PN vs PNN	Nonsense	−6.44656	3.119E-10	1.559E-08	TRUE
PN vs PNN	raw pairs passed	15.95968	1.747E-47	0.000E + 00	TRUE
PN vs PNN	r1_maxlength	3.883107	1.138E-04	5.446E-03	TRUE
PN vs PNN	r2_maxlength	3.883107	1.138E-04	5.446E-03	TRUE
PN vs PNN	r1_numseqs	2.021773	4.358E-02	8.161E-01	FALSE
PN vs PNN	r2_numseqs	2.021773	4.358E-02	8.161E-01	FALSE
PN vs PNN	r1_minlength	0.927906	3.538E-01	1.000E + 00	FALSE
PN vs PNN	r2_minlength	−0.5458	5.854E-01	1.000E + 00	FALSE
PN vs PNN	r1_gc	−0.26695	7.896E-01	1.000E + 00	FALSE
PN vs PNN	r2_gc	−0.90928	3.635E-01	1.000E + 00	FALSE
PN vs PNN	r1_qual	0.559492	5.760E-01	1.000E + 00	FALSE
PN vs PNN	r2_qual	3.245425	1.234E-03	5.290E-02	FALSE
PN vs FN	Primer dimer	−1.03201	3.207E-01	9.999E-01	FALSE
PN vs FN	Ambiguity	−1.51352	1.333E-01	9.881E-01	FALSE
PN vs FN	Short read	−1.47375	1.586E-01	9.944E-01	FALSE
PN vs FN	MID mismatch	−5.29945	1.447E-04	6.634E-03	TRUE
PN vs FN	Minority MID	−13.2917	1.590E-24	0.000E + 00	TRUE
PN vs FN	Primer verification	−2.51412	1.338E-02	4.321E-01	FALSE
PN vs FN	Casper mismatch	−1.91524	7.643E-02	9.381E-01	FALSE
PN vs FN	Nonsense	−0.52093	6.037E-01	1.000E + 00	FALSE
PN vs FN	raw pairs passed	2.537808	2.448E-02	6.290E-01	FALSE
PN vs FN	r1_maxlength	0.388275	7.045E-01	1.000E + 00	FALSE
PN vs FN	r2_maxlength	0.388275	7.045E-01	1.000E + 00	FALSE
PN vs FN	r1_numseqs	0.79751	4.400E-01	1.000E + 00	FALSE
PN vs FN	r2_numseqs	0.79751	4.400E-01	1.000E + 00	FALSE
PN vs FN	r1_minlength	−1.71001	9.675E-02	9.686E-01	FALSE
PN vs FN	r2_minlength	−0.98698	3.430E-01	1.000E + 00	FALSE
PN vs FN	r1_gc	0.433694	6.711E-01	1.000E + 00	FALSE
PN vs FN	r2_gc	0.353036	7.286E-01	1.000E + 00	FALSE
PN vs FN	r1_qual	−0.67196	5.144E-01	1.000E + 00	FALSE
PN vs FN	r2_qual	0.15547	8.790E-01	1.000E + 00	FALSE

P pass, F fail, PN passing negative, PNN passing non-negative, FN failing negative

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