Table 1 General next-generation sequencing metrics and mutational burden.

CN	Comp	Cell (%)	MR	Q30%	TMB
1	Normal	100	157	97	6.844
1	IM	~50	149	97	5.323
2	Normal	100	200	96	5.323
2	IM	~50	286	98	6.083
3	IM	~20	260	98	4.562
4	IM	~30	241	97	4.562
5	IM	~80	263	98	5.323
6	Normal	100	298	97	3.042
6	IM	~80	248	98	3.802
7	Normal	100	102	96	0.76
7	IM	~80	129	95	0.76
8	Normal	100	341	98	5.323
8	IM	~80	264	97	3.042
9	Normal	100	289	98	3.802
9	IM	~80	260	98	3.802
10	Normal	100	306	98	3.042
10	IM	~80	279	98	3.802
11	Normal	100	285	98	0.76
11	IM	~80	244	98	0.76
12	IM	~50	203	97	1.521
13	IM	~80	196	98	4.562
14	IM	~80	222	98	2.281
15	Normal	100	118	96	0.76
15	IM	~80	126	96	1.521
16	Normal	100	100	95	4.562
16	IM	~80	90	93	4.562
17	IM	~80	247	98	3.802
18	Normal	100	200	97	4.562
18	IM	~50	250	98	4.562
19	IM/D	~70	174	96	1.521
20	IM/D	~40	249	98	6.083
20	AdenoCa	~40	346	98	5.323
21	IM/D	~20	202	97	20.531
21	High-grade UC	~50	209	98	25.094
22	IM/D^a	~50	243	97	7.604
23	IM/D^a	~20	202	97	3.802

AdenoCa adenocarcinoma, Cell estimated cellularity, CN case number, Comp histologic component, IM intestinal metaplasia, IM/D intestinal metaplasia with dysplasia, MR mean number of aligned high-quality reads, Q30% Percentage of exons having more than 30 aligned reads, TMB mutational burden (in mutations per Mb), UC urothelial carcinoma.
^aIn these cases, the differential diagnosis was between intestinal metaplasia with high-grade dysplasia and superficial fragments of adenocarcinoma (no clear evidence of invasion in the sample) or adenocarcinoma in situ.

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