A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Koboldt, Daniel C; Staisch, Julia; Thillainathan, Bavithra; Haines, Karen; Baird, Scott E; Chamberlin, Helen M; Haag, Eric S; Miller, Raymond D; Gupta, Bhagwati P

doi:10.1186/1471-2164-11-236

BMC Genomics

Table 4 List of small indels tested by PCR.

From: A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae

Chr	Indel ID	Location (cM)	Ultra_contig	Predicted indel size (bp)	Predicted amplicon		Status
					AF16	HK104
1	bhP41	unknown	cb25.fpc4180	16	242	258	Inconsistent products
	bhP42	unknown	cb25.fpc4184	15	252	267	True
	bhP19	0.7	cb25.fpc2695	32	247	215	True
	bhP43	14	cb25.fpc3857b	12	245	257	Multiple products
	bhP7	28.6	cb25.fpc2032	7	246	239	True
	bhP1	29.2	cb25.fpc3441	10	250	260	True
	bhP29	~52	cb25.fpc4140	17	248	231	True
2	bhP20	2.4	cb25.fpc4168	21	248	227	Inconsistent products
	bhP6	~8	cb25.fpc0071	11	973	962	True
	bhP2	~10	cb25.fpc3052a	7	243	236	True
	bhP33	~10	cb25.fpc3052a	44	245	201	Inconsistent products
	bhP28	11.9-13.1	cb25.fpc0011	22	249	227	Inconsistent products
	bhP32	11.9-13.1	cb25.fpc0011	21	250	271	True
	bhP21	23.3-28.6	cb25.fpc0058	20	251	231	True
	bhP44	~38	cb25.fpc1402a	12	312	324	Failed PCR in HK104
	bhP8	49.9	cb25.fpc0305	18	249	231	True
3	bhP18	0	cb25.fpc4010	8	248	256	True
	bhP14	12.5	cb25.fpc4153	22	241	219	True
	bhP38	16.8-17.5	cb25.fpc2187	44	249	293	True
	bhP12	21.2	cb25.fpc2976	29	248	219	True
	bhP34	21.8	cb25.fpc2976	7	246	239	True
	bhP39	25.7	cb25.fpc0201	13	250	263	Multiple products
	bhP40	30	cb25.fpc0002	20	250	270	True
	bhP10	35.4	cb25.fpc4224	11	249	238	No indel
4	bhP13	1.9-5.1	cb25.fpc3752	14	250	264	True
	bhP15	7.9	cb25.fpc4250	20	250	270	True
	bhP45	17.6	cb25.fpc4260	20	245	265	True
	bhP4	18.2-18.8	cb25.fpc0039	9	250	241	Inconsistent products
	bhP11	20.6	cb25.fpc4090	18	251	233	True
	bhP9	31	cb25.fpc1570	16	256	272	True
	bhP16	43.5	cb25.fpc0107	21	251	230	True
	bhP30	57.8	cb25.fpc3052b	20	248	262	Inconsistent products
	bhP46	57.8	cb25.fpc3052b	10	242	252	Multiple products
5	bhP22	1.9	cb25.fpc4095	14	249	263	Inconsistent products
	bhP31	2.5-3.2	cb25.fpc2114	24	244	268	True
	bhP47	9.6	cb25.fpc2887a	21	243	222	True
	bhP37	18.9	cb25.fpc4470	10	251	261	True
	bhP5	26.7	cb25.fpc0090	16	291	275	True
	bhP23	26.7	cb25.fpc0090	22	250	228	Multiple products
	bhP48	40.2-40.8	cb25.fpc4063	22	249	271	True
	bhP24	56.9	cb25.fpc0129	16	242	258	True
X	bhP25	8.4	cb25.fpc0045	32	250	218	True
	bhP36	13.6-16.3	cb25.fpc4044b	11	244	255	True
	bhP26	21-21.7	cb25.fpc0106	22	251	229	True
	bhP49	34.1	cb25.fpc0829	14	250	264	True

The table is organized similar to Table 3. The "Status" column shows whether an indel was correctly verified by PCR (True) or not (False). In all cases DNA sizes were determined by visual inspection.

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ISSN: 1471-2164

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