Next-generation sequencing traces human induced pluripotent stem cell lines clonally generated from heterogeneous cancer tissue

Table 3 Mapped reads

	NCC1	CC1	CC1-1	CC1-2	CC1-7	CC1-8	CC1-9	CC1-11	CC1-12	CC1-17	CC1-18	CC1-25
No. of total reads ①	36293880	33194872	25884264	35229732	29374016	34360658	33091570	30693498	30562538	37760584	39237616	30757110
No. of mapped reads ② (③+ ④ + ⑤)	36210841	33066194	25545096	34845596	28911555	33842665	32976780	29898986	30464308	36670526	38078508	30173511
No. of mapped reads with Paired-End ③	26935180	26333748	21884450	25981140	21498822	26807330	26704280	25386830	25103580	29513694	30869186	21622036
No. of mapped reads with Single-End ④	15741	24050	14051	16508	12336	17984	14651	27429	14354	27336	25456	19687
No. of discarded reads1 ⑤	9259920	6708396	3646595	8847948	7400397	7017351	6257849	4484727	5346374	7129496	7183866	8531788
No. of unmapped reads (①‐②)	83039	128678	339168	384136	462461	517993	114790	794512	98230	1090058	1159108	583599
No. of effective reads (③ + ④)	26950921	26357798	21898501	25997648	21511158	26825314	26718931	25414259	25117934	29541030	30894642	21641723

¹Discarded reads were as follows: Reads mapped to chromosomes other than the target; Reads where each paired-end is mapped to a different chromosome; Reads not used for single-nucleotide variant/InDel detection such as PCR duplicates. Each number of ② consists of each total number of "③ plus ④ plus ⑤"; "① - ②" means "each number of ① minus each number of ②"; "③ + ④" means "each number of ③ plus each number of ④". NCC1: The matched adjacent non-cancerous tissue; CC1: The starting cancer tissue of the iPSC lines; CC1-1 to CC1-25: Each induced pluripotent stem cell line.