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Medium Indels (Koboldt et al. BMC Genomics 2010)

Table 3 from the paper (DOI: 10.1186/1471-2164-11-236)

Chr	Indel ID	Location (cM)	Ultra_contig	AF16 amplicon (bp) predicted	AF16 amplicon (bp) observed	HK104 amplicon (bp) predicted	HK104 amplicon (bp) observed	Predicted indel	Validation status	Validation type
1	cb-m142	12.6	cb25.fpc4321	665	700	915	950	250 bp insertion	250 bp insertion	*
	cb-m2	13.4	cb25.fpc4321	1461	Failed PCR	1125	Failed PCR	336 bp deletion	Failed PCR
	cb-m5	20.0	cb25.fpc4171	774	750	674	Failed PCR	100 bp deletion	Failed PCR
	cb-m5	20.0	cb25.fpc4171	461	500	361	500	100 bp deletion	no indel
	cb-m6	43.9	cb25.fpc4140	930	900	785	1000	145 bp deletion	100 bp insertion	**
	cb-m13	unknown	cb25.fpc0078	504	420	385	400	119 bp deletion	20 bp deletion	**
	cb-m14	unknown	cb25.fpc4127	1000	1000	676	710	324 bp deletion	290 bp deletion	*
	cb-m146	unknown	cb25.fpc4122	406	480	506	530	100 bp insertion	50 bp insertion	**
	cb-m12	unknown	cb25.fpc4127	921	Failed PCR	416	1000	505 bp deletion	Failed PCR
2	cb-m21	24.2	cb25.fpc0058	825	900	670	700	155 bp deletion	200 bp deletion	*
	cb-m16	37.4	cb25.fpc4071	1097	>1500	687	>1500	410 bp deletion	unclear
	cb-m19	11.9-13.1	cb25.fpc0011	1364	1013	828	750	536 bp deletion	263 bp deletion	**
	cb-m149	27.9-34.0	cb25.fpc4206	470	490	603	600	133 bp insertion	110 bp insertion	*
	cb-m26	27.9-34.0	cb25.fpc4206	678	700	407	410	271 bp deletion	290 bp deletion	*
	cb-m38	unknown	cb25.fpc4131	835	860	544	600	291 bp deletion	260 bp deletion	*
	bdP4	unknown	cb25.fpc2441	1013	~990	903	~880	110 bp deletion	110 bp deletion	*
3	cb-m46	6.1	cb25.fpc2587	747	1020	574	750	173 bp deletion	270 bp deletion	*
	cb-m155	6.1	cb25.fpc2587	1169	Failed PCR	1329	Failed PCR	160 bp insertion	Failed PCR
	cb-m48	21.2	cb25.fpc2976	1163	1200	644	1200	519 bp deletion	no indel
	cb-m205	25.8	cb25.fpc4079	671	700	971	1000	300 bp insertion	300 bp insertion	*
	cb-m159	36.5	cb25.fpc4224	463	500	655	Failed PCR	192 bp insertion	Failed PCR
	cb-m160	28.8-29.3	cb25.fpc2193	821	1000	1053	1200	232 bp insertion	200 bp insertion	*
	bdP1	31.3	cb25.fpc0002	1723	~1700	~1500	~1500	~200 bp deletion	200 bp deletion	*
4	cb-m172	18.2	cb25.fpc0039	650	700	904	950	254 bp insertion	250 bp insertion	*
	cb-m170	20.6	cb25.fpc4090	691	720	931	Failed PCR	240 bp insertion	Failed PCR
	cb-m171	25.5	cb25.fpc4132	381	450	476	550	95 bp insertion	100 bp insertion	*
	cb-m70	25.5	cb25.fpc4132	594	>1600	421	1600	173 bp deletion	very large indel	**
	cb-m176	37.5-41.2	cb25.fpc3835	732	Failed PCR	1014	Failed PCR	282 bp insertion	Failed PCR
	cb-m74	37.5-41.2	cb25.fpc3835	677	1000	523	700	154 bp deletion	300 bp deletion	**
	cb-m76	42.4-43.0	cb25.fpc2328	709	900	527	550	182 bp deletion	350 bp deletion	**
	cb-m177	9.2-9.8	cb25.fpc4118	801	800	946	900	145 bp insertion	100 bp insertion	*
	cb-m179	unknown	cb25.fpc4331	383	450	500	520	117 bp insertion	70 bp insertion	*
5	cb-m103	19.0	cb25.fpc2220	600	700	454	500	146 bp deletion	200 bp deletion	*
	cb-m97	46.1	cb25.fpc4109	591	705	392	490	199 bp deletion	215 bp deletion	*
	cb-m105	37.0-37.7	cb25.fpc4063	692	800	454	520	238 bp deletion	280 bp deletion	*
	cb-m104	37.0-37.7	cb25.fpc4063	942	Failed PCR	661	Failed PCR	281 bp deletion	Failed PCR
X	cb-m197	3.5	cb25.fpc4033	692	700	855	790	163 bp insertion	90 bp insertion	*
	cb-m204	17.4	cb25.fpc4044	689	750	949	1000	260 bp insertion	250 bp insertion	*
	cb-m136	30.1	cb25.fpc0829	1440	2000	645	750	795 bp deletion	1250 bp deletion	*
	cb-m127	34.1	cb25.fpc2334	486	600	349	405	137 bp deletion	195 bp deletion	*
	cb-m126	34.1	cb25.fpc2334	785	Failed PCR	648	Failed PCR	137 bp deletion	Failed PCR
	cb-m135	27.4-34.1	cb25.fpc0829	720	900	584	Failed PCR	136 bp deletion	Failed PCR

The indels are arranged by chromosome and location. The corresponding ultracontigs are also listed. The “unknown” locations refer to unassembled contigs. The predicted indel sizes are based on in silico analysis of AF16 and HK104 amplicons. The validation type column marks indels that were consistent with prediction () and those that differed significantly (*).

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