Table 9 Comparison of subtyping results for avian influenza viruses from sample set 1, 3, 4 and 5, with subtypes generated by flui automated pipeline and by manually mapping to a GISAID reference gene set. [+] indicates that the sequencing reads passed the quality thresholds, and the generated subtype agrees with the known subtype. [—] indicates that sequencing reads did not pass the quality thresholds and hence a subtype could not be called. In Bold indicates disagreement between passed or failed reads in between both methods.

Sample	Location	Sample type	Known subtype	HA		NA
Sample	Location	Sample type	Known subtype	GISAID mapping	Flui	GISAID mapping	Flui
1	Kaituna	Isolate	H4N2	+	+	+	+
2	Turua	Isolate	H5N7	+	+	+	+
3	Lake Te Rotokare	Isolate	H4N6	+	+	+	+
4	Lake Te Rotokare	Isolate	H3N8	+	+	+	+
5	Lake Aniwhenua	Isolate	H12N5	+	+	+	+
6	Lake Aniwhenua	Isolate	H5N2	+	+	+	+
8	Kaituna	Isolate	H5N3	+	+	+	+
10	Kaituna	Isolate	H3N1	+	+	+	+
13a	Otago, poultry farm	Swab-Qiagen	H7N6	+	+	+	+
14a	Otago, poultry farm	Swab-Qiagen	H7N6	+	+	+	+
15a	Otago, poultry farm	Swab-Qiagen	H7N6	+	+	+	+
16a	Otago, poultry farm	Swab-Qiagen	H7N6	+	+	+	+
17a	Otago, poultry farm	Swab-Qiagen	H7N6	+	—	+	+
13b	Otago, poultry farm	Swab-Zymo	H7N6	+	+	+	+
14b	Otago, poultry farm	Swab - Zymo	H7N6	+	+	+	+
15b	Otago, poultry farm	Swab- Zymo	H7N6	—	—	+	+
16b	Otago, poultry farm	Swab- Zymo	H7N6	—	—	—	—
17b	Otago, chicken farm	Swab- Zymo	H7N6	—	—	—	—
18	Te Awamutu	Isolate	H6N2	+	+	+	+
19	Paeroa	Isolate	H4N6	–	–	+	+
20	Kaituna	Isolate	H3N1	+	+	+	+
22	Paeroa	Isolate	H3N8	+	+	+	+
23	Turua	Isolate	H1N2	+	—	+	+
24	Paeroa	Isolate	H3N2	+	+	+	+
25	Kerepehi	Isolate	H10N3	+	+	+	+
26	Kerepehi	Isolate	H4N6	+	+	+	+
27	Gisborne	Isolate	H4N2	+	+	+	+
Number of samples that passed quality threshold and classified as known subtype				23/27	21/27	25/27	25/27
Kappa agreement				Kappa = 0.76		Kappa = 1.0

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