TABLE 1.

Total Reads, Reads Mapping to Sarcomatome, Read Coverage at Breakpoint (BP), and Breakpoint Spanning Reads (Fusion Reads)

Sample	Total Reads	Sarcomatome†	BP Coverage	Fusion Reads*
SS_F	8,202,680	112,177	25	18
SS_16	7,882,763	217,304	24	16
SS_31	6,151,281	77,483	22	8
SS_34	5,981,106	140,866	18	10
MLS_09	7,388,216	37,774	24	13
MLS_10	6,644,348	58,769	3	1
MLS_10_H	78,267,719	652,826	35	12
MLS_11	6,616,442	42,326	8	4
MLS_11_H	79,086,356	478,212	40	18
EWS_32	7,681,341	280,025	0	0
EWS_32_r	9,307,446	101,848	12	1
EWS_32_H	214,962,075	7,012,482	146	9
EWS_35	6,820,639	72,021	0	0
CCS_33	5,450,583	37,867	3	2
CCS_33_H	202,231,159	1,248,442	65	35

^*Breakpoint spanning reads.

^†Pairs mapping to sarcomatome (proper and discordant).

_H indicates HiSeq; _r, ribodepleted.