Comparative performance of the GenoLab M and NovaSeq 6000 sequencing platforms for transcriptome and LncRNA analysis

Liu, Yongfeng; Han, Ran; Zhou, Letian; Luo, Mingjie; Zeng, Lidong; Zhao, Xiaochao; Ma, Yukun; Zhou, Zhiliang; Sun, Lei

doi:10.1186/s12864-021-08150-8

Table 2 Summary of SNP identifcation in all samples

From: Comparative performance of the GenoLab M and NovaSeq 6000 sequencing platforms for transcriptome and LncRNA analysis

Sample	A- > G	G- > A	C- > T	T- > C	Transition	A- > C	C- > A	A- > T	T- > A	C- > G	G- > C	G- > T	T- > G	Transversion	Total
Bean_mRNA_AB_N	13,754	13,281	13,327	13,609	53,971	4549	4512	6766	6591	3330	3342	4450	4538	38,078	92,049
Bean_mRNA_VZ_N	13,260	12,819	12,938	13,308	52,325	4381	4402	6479	6294	3260	3277	4268	4414	36,775	89,100
Bean_mRNA_YS_N	13,360	12,847	12,998	13,244	52,449	4339	4409	6552	6401	3268	3275	4336	4472	37,052	89,501
Bean_mRNA_AB_G	13,267	12,816	12,876	13,047	52,006	4357	4425	6772	6430	3213	3214	4337	4416	37,164	89,170
Bean_mRNA_VZ_G	15,421	14,791	14,768	15,323	60,303	4991	5084	7545	7311	3787	3796	4997	5031	42,542	102,845
Bean_mRNA_YS_G	12,393	11,956	11,975	12,390	48,714	4050	4093	6223	6012	3024	2989	4050	4056	34,497	83,211
Human_mRNA_AB_N	28,147	19,847	19,745	27,765	95,504	4212	4279	3205	3296	5208	5153	4161	4283	33,797	129,301
Human_mRNA_TG_N	26,667	19,444	19,386	26,452	91,949	4069	4152	3028	3060	5298	5168	4101	4049	32,925	124,874
Human_mRNA_VZ_N	23,206	18,098	17,877	23,211	82,392	3825	3865	2824	2803	5035	4889	3830	3850	30,921	113,313
Human_mRNA_YS_N	18,333	15,280	15,253	18,499	67,365	3134	3255	2322	2279	4172	4038	3204	3199	25,603	92,968
Human_mRNA_AB_G	22,677	18,164	17,955	22,700	81,496	3785	3797	3340	3365	4702	4605	3799	3840	31,233	112,729
Human_mRNA_TG_G	17,891	14,885	14,971	17,824	65,571	3101	3146	2778	2740	3963	3825	3080	3164	25,797	91,368
Human_mRNA_VZ_G	28,066	23,315	23,117	28,012	102,510	4978	5198	4612	4653	6187	6016	5126	5004	41,774	144,284
Human_mRNA_YS_G	16,090	14,008	13,905	16,040	60,043	2971	3000	2509	2466	3760	3681	2886	3027	24,300	84,343
Mouse_mRNA_AB_N	1868	1186	1205	1833	6092	342	386	428	460	362	377	372	340	3067	9159
Mouse_mRNA_VZ_N	2612	1416	1484	2582	8094	424	448	548	531	403	371	457	408	3590	11,684
Mouse_mRNA_YS_N	1998	1311	1263	1989	6561	346	400	387	401	312	274	363	314	2797	9358
Mouse_mRNA_AB_G	2252	1328	1402	2100	7082	428	456	1069	1025	381	379	439	400	4577	11,659
Mouse_mRNA_VZ_G	2871	1721	1687	2778	9057	620	809	1189	1109	538	524	818	632	6239	15,296
Mouse_mRNA_YS_G	2054	1063	1046	1902	6065	296	253	711	719	273	268	291	270	3081	9146

Note: A- > G means base A mutation as base G, Transition are interchanges of two-ring purines (A- > G and G- > A) or of one-ring pyrimidines (C- > T and T- > C), Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures. AB_, VZ_, YS_,TG_ means library kits from four companies, N and G means Novaseq 6000 and GenoLab M

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ISSN: 1471-2164

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