Table 1. Comparison between Novoalign and BWA mapping algorithms.

			Numbers of SNPs by allele frequency (AF)
Mapper	Minimum variant reads	SNP type	0.05–0.1	0.1–0.2	0.2–0.3	0.3–0.4	0.4–0.5	0.5–0.6	0.6–0.7	0.7–0.8	0.8–0.9	0.9–1.0	SNPs (total)	SNPs (AF>0.1)
Novoalign	3	EMS	1357	545	199	123	68	42	35	28	24	248	2669	1312
		NON-EMS	1360	658	124	38	7	2	2	1	1	6	2199	839
BWA	3	EMS	1105	429	150	99	61	48	31	25	24	251	2223	1118
		NON-EMS	1039	469	92	28	9	3	3	1	1	6	1651	612
Novoalign	4	EMS	477	289	137	93	68	42	35	28	24	248	1441	964
		NON-EMS	551	327	64	20	7	2	2	1	1	6	981	430
BWA	4	EMS	370	212	112	87	61	48	31	25	24	251	1221	851
		NON-EMS	439	238	40	20	9	3	3	1	1	6	760	321
Novoalign	5	EMS	214	155	110	76	63	42	35	28	24	248	995	781
		NON-EMS	233	144	39	12	4	2	2	1	1	6	444	211
BWA	5	EMS	175	115	93	78	56	48	31	25	24	251	896	721
		NON-EMS	241	122	25	11	3	3	3	1	1	6	416	175
Novoalign	6	EMS	118	94	94	67	61	41	33	28	24	248	808	690
		NON-EMS	136	80	24	9	4	2	2	1	1	6	265	129
BWA	6	EMS	88	63	83	71	54	46	31	25	24	251	736	648
		NON-EMS	122	58	21	8	3	2	3	1	1	6	225	103
Novoalign	7	EMS	72	58	83	64	60	39	33	23	24	248	704	632
		NON-EMS	79	47	15	5	4	2	2	1	1	6	162	83
BWA	7	EMS	52	40	77	63	53	46	30	24	24	251	660	608
		NON-EMS	81	32	16	6	3	2	3	1	1	6	151	70
Novoalign	8	EMS	53	38	71	61	55	34	31	22	23	231	619	566
		NON-EMS	52	33	10	4	3	1	1	0	1	6	111	59
BWA	8	EMS	33	28	67	58	47	42	27	23	24	238	587	554
		NON-EMS	53	26	10	2	3	2	1	1	1	6	105	52

The Novoalign and BWA-MEM mapping algorithms were tested using the IWGSC wheat Chromosome Arm Survey Sequence reference showing total numbers of SNPs detected at different minimum variant read numbers and allele frequencies. EMS mutations are defined at G>A and C>T transitions.