ID	Gene	Exon(s)	"Mean Coverage"	"Barnacle + BWA"	"Barnacle-MM + BWA"	"Barnacle + ABySS-map"	"Barnacle-MM + ABySS-map"	Notes
ptd92	CDK5RAP1	exon7-exon13	0.187627	N	N	N	N	mean coverage below read-support threshold
ptd85	CHADL	exon2-exon4	0.493653	N	N	N	N	mean coverage below read-support threshold
ptd23	PPPDE2	exon2	0.548849	N	N	N	N	mean coverage below read-support threshold
ptd71	UBE2C	exon2-exon3	0.584846	N	N	N	N	mean coverage below read-support threshold
ptd17	UFD1L	exon3-exon5	0.609442	N	N	N	N	mean coverage below read-support threshold
ptd37	RP5-983L19.1	exon2	0.72659	N	N	N	N	mean coverage below read-support threshold
ptd83	COMT	exon2-exon3	0.818823	N	N	N	N	mean coverage below read-support threshold
ptd48	NPEPL1	exon3-exon6	0.896243	N	N	N	N	mean coverage below read-support threshold
ptd2	RP4-715N11.2	exon3	0.964172	N	N	N	N	mean coverage below read-support threshold
ptd13	SMTN	exon4-exon8	1.075299	N	N	N	N	mean coverage below read-support threshold
ptd45	GGT2	exon4-exon10	1.24997	N	N	N	N	mean coverage below read-support threshold
ptd66	PACSIN2	exon2	1.291077	N	N	N	N	mean coverage below read-support threshold
ptd15	TCEA2	exon2	1.667873	N	N	N	N	mean coverage below read-support threshold
ptd40	LARGE	exon2	1.683838	N	N	N	N	mean coverage below read-support threshold
ptd62	CPT1B	exon8	1.907568	N	N	N	N	mean coverage below read-support threshold
ptd21	OSBP2	exon2-exon4	2.105622	N	N	N	N	mean coverage below read-support threshold
ptd30	GTPBP1	exon2	2.425468	N	N	N	N	mean coverage below read-support threshold
ptd36	TMEM211	exon2	2.597079	N	N	N	N	mean coverage below read-support threshold
ptd44	NPEPL1	exon10	3.151656	N	N	N	N	mean coverage below read-support threshold
ptd89	TMPRSS6	exon4-exon8	3.251978	N	N	N	N	mean coverage below read-support threshold
ptd69	INPP5J	exon11	3.403498	N	N	N	N	mean coverage below read-support threshold
ptd81	C22orf36	exon2	3.62418	N	N	N	N	mean coverage below read-support threshold
ptd39	CITF22-24E5.1	exon2	3.689984	N	N	N	N	mean coverage below read-support threshold
ptd32	ENTHD1	exon2-exon6	4.206751	N	N	N	N	mean coverage below read-support threshold
ptd72	L3MBTL2	exon3-exon4	4.691194	N	N	N	N	mean coverage below read-support threshold
ptd64	C20orf112	exon5-exon6	4.710923	N	N	N	N	mean coverage below read-support threshold
ptd46	GGTLC2	exon2-exon3	5.423827	N	N	N	N	
ptd38	ST13	exon2	7.251906	N	N	N	N	
ptd28	OSBP2	exon2-exon3	10.213675	N	N	N	N	
ptd98	SYNGR1	exon2-exon3	10.363352	N	N	Y	Y	
ptd18	RP3-477H23.3	exon2	10.663519	N	N	Y	Y	
ptd91	RP1-191L6.2	exon2	12.95723	N	N	N	N	
ptd56	LL22NC03-80A10.6	exon2-exon5	14.742208	N	N	N	N	
ptd35	GGT1	exon13-exon15	14.986942	N	N	N	N	
ptd63	DEPDC5	exon7-exon15	16.282425	Y	Y	Y	Y	
ptd34	PREX1	exon3-exon35	16.602998	Y	Y	Y	Y	
ptd84	STAU1	exon11	17.037888	N	N	N	N	
ptd26	GAS2L1	exon3-exon4	17.156913	Y	Y	Y	Y	
ptd20	KB-1183D5.12	exon2	18.026769	N	N	N	N	
ptd55	ERGIC3	exon2	18.370576	N	N	N	N	
ptd25	EIF4ENIF1	exon3	24.430462	N	N	N	N	reported as ITD due to incorrect exon boundary counting
ptd29	LIME1	exon2-exon4	25.818956	Y	Y	Y	Y	
ptd50	COL20A1	exon31	27.028347	N	N	N	N	reported as ITD due to incorrect exon boundary counting
ptd42	PIGT	exon2	27.032136	N	N	N	N	
ptd97	C22orf25	exon2-exon5	27.899448	Y	Y	Y	Y	
ptd86	DERL3	exon2-exon4	32.61028	Y	Y	Y	Y	
ptd90	RP5-843L14.1	exon2	33.272826	Y	Y	Y	Y	
ptd16	LPIN3	exon8-exon9	33.460072	N	N	N	N
ptd31	RP3-477H23.3	exon3-exon4	34.520384	Y	Y	Y	Y
ptd61	DERL3	exon5	35.594011	Y	Y	Y	Y
ptd4	HNF4A	exon3	37.160963	N	N	N	N
ptd3	ANKRD54	exon3	37.567419	N	N	N	N
ptd96	CYTSA	exon2	37.667827	N	N	N	N
ptd77	SERHL2	exon2-exon4	37.746255	N	N	N	N
ptd0	RP11-410N8.4	exon2	39.00484	N	N	N	N
ptd11	RP5-907D15.2	exon2-exon3	40.955643	Y	Y	Y	Y
ptd87	TTPAL	exon3-exon5	42.76366	Y	Y	Y	Y
ptd41	CTA-373H7.7	exon2	42.886211	Y	Y	Y	Y
ptd53	ZNF133	exon4-exon5	47.401514	Y	Y	Y	Y
ptd75	BIRC7	exon2-exon5	48.762622	Y	Y	Y	Y
ptd94	TXNRD2	exon2	49.575293	N	N	N	N
ptd22	SFI1	exon3	50.781222	N	N	N	N
ptd65	PTPRA	exon3-exon4	51.305345	Y	Y	Y	Y
ptd43	CYTH4	exon3-exon4	52.897697	N	N	N	N	
ptd60	C20orf177	exon2-exon3	55.701098	N	N	N	N	
ptd88	C20orf95	exon2-exon7	63.118098	Y	Y	Y	Y	
ptd70	UNC84B	exon5-exon11	68.123211	Y	Y	Y	Y	
ptd79	APOL1	exon2-exon3	69.345022	N	N	N	N	
ptd76	NECAB3	exon3-exon7	69.452878	Y	Y	Y	Y	
ptd6	RANBP1	exon2	70.223325	Y	Y	Y	Y	
ptd57	TRMT6	exon4-exon7	74.501301	Y	Y	Y	Y	
ptd78	ZMAT5	exon2-exon4	76.77012	Y	Y	Y	Y	
ptd10	AL355392.1	exon3-exon5	84.813488	Y	Y	Y	Y	
ptd52	DDX27	exon4	88.199641	Y	Y	Y	Y	
ptd74	TFIP11	exon10-exon11	95.430262	Y	Y	Y	Y	
ptd67	C1QTNF6	exon5	103.802571	N	N	N	N	
ptd7	KCNQ2	exon2-exon11	115.138163	Y	Y	Y	Y	
ptd49	UBE2C	exon3	116.529208	N	N	N	N	BLAT fails to report one of overlapping alignments for junction contig
ptd14	KB-1183D5.13	exon2	128.926638	N	N	N	N	"gene is in highly duplicated region of the genome, causing poor contig-to-genome alignments"
ptd47	GNAS	exon2	129.295993	N	N	N	N	
ptd82	MKL1	exon2-exon4	150.752791	N	N	N	N	simulated event uses exon boundary not in current annotations
ptd58	C20orf12	exon15-exon20	185.84984	Y	Y	Y	Y	
ptd8	C20orf112	exon5-exon6	191.566807	Y	Y	N	N	
ptd54	LARGE	exon7-exon12	199.132983	N	N	N	N	incorrect exon boundary counting
ptd33	CSF2RB	exon2-exon3	204.489383	Y	Y	Y	Y	
ptd80	SLC35C2	exon4	249.365684	Y	Y	Y	Y	
ptd1	NCOA5	exon3-exon5	264.535292	Y	Y	Y	Y	
ptd73	KB-1183D5.13	exon2-exon6	272.923603	N	N	N	N	"gene is in highly duplicated region of the genome, causing poor contig-to-genome alignments"
ptd59	AP000354.3	exon3-exon4	354.002548	N	N	N	N	BLAT fails to report one of overlapping alignments for junction contig
ptd95	SMCR7L	exon2	357.747416	Y	Y	Y	Y	
ptd12	RP4-695O20__B.10	exon3	364.601672	N	N	N	N	reported as ITD due to incorrect exon boundary counting
ptd68	TRPC4AP	exon3-exon16	420.182309	Y	Y	Y	Y	
ptd93	SERHL	exon6-exon7	441.55419	N	N	N	N	tandem duplication of full gene in reference genome allows collinear alignment of contig with exon duplication
ptd24	WFDC5	exon2-exon3	587.204695	Y	Y	Y	Y	
ptd51	HNF4A	exon6-exon7	713.614311	Y	Y	Y	Y	
ptd27	ADAM33	exon7-exon9	757.852643	Y	Y	Y	Y	
ptd99	GNAS	exon6-exon9	875.799195	Y	Y	N	N	
ptd5	CENPM	exon2-exon4	999.685327	Y	Y	Y	Y	
ptd9	MB	exon2	1365.878761	Y	Y	Y	Y	
ptd19	MIAT	exon3	1478.855655	N	N	N	N	BLAT fails to report one of overlapping alignments for junction contig