TABLE 2.

Enrichment of RAD markers in bulk segregant analysis

Array elementa	Contigb	Basec	LGd	Parental replicate 1e	Parental replicate 2f	Averageg	Bulk #1h	Bulk #2i	Averagej	Relative enrichmentk
NCU01012.1	7.15	8E+05	LG V	−1.78	−3.46	−2.62	−1.40	−1.07	−1.23	0.47
NCU01048.1	7.15	7E+05	LG V	−3.84	−2.51	−3.17	−1.61	−1.17	−1.39	0.44
NCU01062.1b	7.15	6E+05	LG V	−5.06	−4.90	−4.98	−1.73	−1.66	−1.69	0.34
NCU01127.1	7.15	5E+05	LG V	−2.06	−3.21	−2.63	−1.84	−1.39	−1.62	0.61
NCU01128.1	7.15	5E+05	LG V	−4.47	−4.02	−4.25	−1.93	−1.42	−1.67	0.39
ChIP_Chip_9	7.15	2E+05	LG V	−3.11	−3.58	−3.35	−2.25	−2.06	−2.16	0.64
ChIP_Chip_10	7.15	2E+05	LG V	−3.04	−3.63	−3.33	−2.46	−2.37	−2.41	0.72
ChIP_Chip_11	7.15	2E+05	LG V	−5.11	−5.13	−5.12	−2.84	−1.98	−2.41	0.47
ChIP_Chip_13	7.15	2E+05	LG V	−1.71	−1.03	−1.37	−1.11	−1.32	−1.22	0.89
NCU01381.1	7.14	2E+05	LG V	3.19	5.16	4.18	1.24	2.53	1.89	0.45
NCU01382.1	7.14	2E+05	LG V	4.18	5.01	4.60	1.52	1.41	1.46	0.32
NCU01383.1	7.14	2E+05	LG V	2.41	3.24	2.82	1.21	1.26	1.24	0.44
NCU01384.1	7.14	2E+05	LG V	−3.28	−3.20	−3.24	−2.22	−1.30	−1.76	0.54
NCU06643.1	7.31	3E+05	LG V	1.48	2.83	2.15	1.33	1.20	1.26	0.59
NCU06708.1	7.31	94593	LG V	2.57	2.08	2.33	1.09	2.12	1.60	0.69
NCU06731.1	7.31	20211	LG V	1.99	3.43	2.71	1.34	2.08	1.71	0.63
NCU04112.1	7.13	8E+05	LG V	−2.86	−2.18	−2.52	−2.21	−1.09	−1.65	0.65
NCU04134.1	7.13	7E+05	LG V	1.27	2.29	1.78	1.47	1.30	1.39	0.78
NCU04139.1	7.13	7E+05	LG V	−3.25	−3.07	−3.16	−2.34	−1.77	−2.05	0.65
NCU04186.1	7.13	5E+05	LG V	2.67	3.18	2.93	1.99	1.81	1.90	0.65
NCU04209.1	7.13	5E+05	LG V	−2.22	−2.19	−2.20	−2.16	−1.45	−1.81	0.82
NCU04210.1	7.13	5E+05	LG V	−3.74	−2.24	−2.99	−2.22	−1.48	−1.85	0.62
NCU04213.1	7.13	4E+05	LG V	−2.88	−1.47	−2.17	−1.93	−1.86	−1.89	0.87
NCU04222.1	7.13	4E+05	LG V	−2.11	−2.16	−2.14	−1.89	−1.24	−1.57	0.73
NCU04248.1	7.13	3E+05	LG V	3.42	4.51	3.96	2.52	2.43	2.47	0.62
NCU04274.1	7.13	2E+05	LG V	−2.47	−2.39	−2.43	−1.45	−1.78	−1.61	0.66
NCU04278.1	7.13	2E+05	LG V	−3.64	−2.25	−2.95	−1.70	−1.42	−1.56	0.53
NCU04279.1	7.13	2E+05	LG V	1.49	1.86	1.68	1.22	1.05	1.14	0.68
NCU04298.1	7.13	1E+05	LG V	1.87	2.55	2.21	1.02	1.57	1.29	0.59
NCU08957.1	7.48	1E+05	LG V	−3.72	−2.09	−2.90	−1.24	−1.21	−1.23	0.42
NCU08959.1	7.48	1E+05	LG V	−2.21	−4.93	−3.57	−1.30	−2.08	−1.69	0.47

^aArray element ID was assigned by the Neurospora genome project. Sequence files and additional infomation are available at the FGSC (http://www.fgsc.net).

^bContig numbers are from the Neurospora Genome Sequence Assembly 7 generated by the Broad Institute (http://www.broad.mit.edu/annotation/genome/neurospora/Home.html).

^cThe contig position of the 5′ base of the corresponding oligonucleotide.

^dIndicates linkage of the RAD marker to one of the seven N. crassa linkage groups.

^eThe log₂ (Cy5/Cy3) value from parental replicate 1. RAD tags from N32 were labeled with Cy3 and tags from N3312 were labeled with Cy5.

^fThe log₂ (Cy5/Cy3) value from parental replicate 2. RAD tags from N3312 were labeled with Cy3 and tags from N32 were labeled with Cy5. The values were multiplied by −1.

^gThe average log₂ (Cy5/Cy3) value was calculated from the two replicate parental experiments.

^hThe log₂ (Cy5/Cy3) value from the first bulk segregant experiment. RAD tags from the wild-type pool were labeled with Cy3 and tags from the mutant pool were labeled with Cy5.

ⁱThe log₂ (Cy5/Cy3) value from the second bulk segregant experiment. RAD tags from the wild-type pool were labeled with Cy3 and tags from the mutant pool were labeled with Cy5.

^jThe average log₂ (Cy5/Cy3) value was calculated from the two replicate bulk segregant experiments.

^kThe average log₂ (Cy5/Cy3) value from the bulk segregant experiment was divided by the average log₂(Cy5/Cy3) from the two parental experiments to generate a relative enrichment value.