Online-Only Table 10.

Single cell libraries were prepared using 10X Genomics Chromium Single Cell CNV Solution for CNV profiling.

Sample	total num reads	percent bases R1 Q30	percent bases R2 Q30	correct bc rate	percent non cell barcode	shortest primary contig	percent mappable bins	num cells	total num reads in cells	total num mapped dedup reads in cells	median percent mapped duplicates per cell	mean mapped dedup reads per cell	median effective reads per 1Mbp	median unmapped frac	mean ploidy p25	mean ploidy p50	mean ploidy p75	raw mapd p25	raw mapd p50	raw mapd p75	normalized mapd p25	normalized mapd p50	normalized mapd p75	normalized dimapd p25	normalized dimapd p50	normalized dimapd p75	raw dimapd p25	raw dimapd p50	raw dimapd p75	percent noisy cells	median est cnv resolution mb
TGEN_T1	1,260,880,054	0.93586572	0.84779037	0.87253147	0.03572204	46709983	0.90348588	1465	1060857656	870930774	0.05134489	594491.996	188	0.03222793	2.71181349	2.75221867	2.79193475	0.12499719	0.13813647	0.1566726	0.12499719	0.13813647	0.1566726	0.90367638	0.92666699	0.95082236	0.90367638	0.92666699	0.95082236	0.08395904	1.46801758
TGEN_N1	1,308,946,506	0.94857232	0.86500184	0.86586948	0.05646006	46709983	0.90344055	983	1069386312	817062608	0.12479393	831192.887	255	0.02080845	1.89378524	1.90302472	1.92504924	0.11509274	0.13183257	0.15403324	0.11509274	0.13183257	0.15403324	0.92951399	0.9629042	1.0362302	0.92951399	0.9629042	1.0362302	0.26347915	1.28393555