Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

Table 2 Summary of SNP identification

	Sample	A–G	C–T	Transition	A–C	A–T	C–G	G–T	Transversion	Total
HI-SEQ4000 PE100	1_DMSO_6h_1	264	158	422	84	84	57	71	296	718
	2_DMSO_6h_2	284	186	470	67	74	52	47	240	710
	3_DMSO_6h_3	254	202	456	62	66	49	57	234	690
	4_ABA_6h_1	297	201	498	91	96	58	68	313	811
	5_ABA_6h_2	250	192	442	75	66	42	64	247	689
	6_ABA_6h 3	248	181	429	63	86	43	51	243	672
	Average	266	187	453	74	79	50	60	262	715
BGI-SEQ500 PE100	1_DMSO_6h_1	491	264	755	240	305	49	77	671	1426
	2_DMSO_6h_2	342	177	519	178	244	38	48	508	1027
	3_DMSO_6h_3	460	223	683	323	411	40	67	841	1524
	4_ABA_6h_1	348	217	565	178	256	46	70	550	1115
	5_ABA_6h_2	324	211	535	165	209	41	47	462	997
	6_ABA_6h_3	308	200	508	150	189	31	41	411	919
	Average	379	215	594	206	269	41	58	574	1168
BGI-SEQ500 PE75	1_DMSO_6h_1	384	191	575	295	432	60	128	915	1490
	2_DMSO_6h_2	381	223	604	239	378	64	120	801	1405
	3_DMSO_6h_3	394	191	585	251	362	59	126	798	1383
	4_ABA_6h_1	398	178	576	292	368	57	105	822	1398
	5_ABA_6h_2	349	182	531	210	303	48	90	651	1182
	6_ABA_6h_3	323	167	490	202	273	44	90	609	1099
	Average	372	189	560	248	353	55	110	766	1326

ISSN: 1746-4811