Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA

BMC Genomics

Table 2 KNN accuracy on test data with 5% simulated sequencing error for different sample sizes, test sizes, training sizes and different numbers of neighbors

Test size	Training size	K = 1	K = 2	K = 3	K = 4	K = 5	K = 6	K = 7	K = 8	K = 9	K = 10
Samples of 50 MBases
1	91	0.93	0.93	0.90	0.92	0.90	0.91	0.84	0.85	0.71	0.81
17	75	0.88	0.88	0.84	0.87	0.82	0.83	0.76	0.79	0.71	0.78
32	60	0.86	0.86	0.80	0.83	0.78	0.79	0.74	0.79	0.75	0.82
47	45	0.80	0.80	0.73	0.76	0.69	0.74	0.71	0.76	0.73	0.80
62	30	0.77	0.77	0.68	0.75	0.71	0.77	0.74	0.79	0.78	0.81
77	15	0.66	0.66	0.64	0.68	0.70	0.74	0.74	0.73	0.69	0.67
Samples of 100 MBases
1	91	1.00	1.00	0.98	1.00	1.00	1.00	0.99	0.99	0.82	0.92
17	75	0.99	0.99	0.96	0.98	0.93	0.93	0.86	0.90	0.82	0.88
32	60	0.96	0.96	0.92	0.94	0.87	0.89	0.84	0.87	0.83	0.88
47	45	0.93	0.93	0.87	0.90	0.83	0.87	0.83	0.88	0.83	0.88
62	30	0.86	0.86	0.79	0.84	0.78	0.83	0.80	0.84	0.82	0.85
77	15	0.77	0.77	0.72	0.76	0.73	0.75	0.73	0.72	0.68	0.65
Samples of 300 MBases
1	91	1.00	1.00	1.00	1.00	1.00	1.00	0.98	0.99	0.95	0.98
17	75	1.00	1.00	1.00	1.00	0.98	0.99	0.95	0.97	0.93	0.95
32	60	0.99	0.99	0.97	0.98	0.94	0.95	0.92	0.95	0.93	0.95
47	45	0.98	0.98	0.94	0.95	0.92	0.93	0.91	0.94	0.92	0.95
62	30	0.95	0.95	0.90	0.93	0.90	0.93	0.89	0.91	0.87	0.89
77	15	0.88	0.88	0.84	0.86	0.81	0.82	0.78	0.76	0.72	0.70

ISSN: 1471-2164