Detection of genomic deletions in rice using oligonucleotide microarrays

BMC Genomics

Table 2 Number of deletions predicted on each chromosome in 14 individual IR64 mutants at log ratio < -0.6 for 50% or more probes in a probe set.

Chr	Number of deleted gene models predicted per IR64 mutant line at log ratio < -0.6 for 50% or more probes in a probe set
	d1	D256	D2943	G282^a	G650	G6458	G6489	G6603	G6686	G6728	G7534	G9799	F1856	F2045	Total
1	11	0	0	64	11	0	0	5	2	0	1	0	0	0	30
2	16	0	0	38	16	1	1	4	0	1	2	0	7	1	49
3	7	0	0	37	3	4	4	9	8	4	4	0	0	4	47
4	18	0	0	24	14	3	3	5	1	3	6	0	2	4	59
5	41	0	0	34	12	3	2	6	0	2	5	0	0	2	73
6	9	0	0	20	8	2	2	5	0	2	4	0	0	2	34
7	4	0	1	62	2	1	1	7	1	1	1	0	0	1	20
8	5	0	1	20	8	0	4	4	0	1	2	0	1	0	26
9	9	1	0	21	6	2	2	4	0	2	2	0	0	2	30
10	25	0	0	16	22	4	11	4	1	4	8	1	2	4	86
11	3	0	0	27	0	3	4	8	1	3	5	0	0	3	30
12	20	1	0	26	21	1	1	2	1	1	1	28	28	27	132
Total	168	2	2	359	123	24	35	63	15	24	41	29	40	50	616

^aDeletions predicted for G282 are not included in totals. Because the number of predictions is large, to reduce FPR, a higher stringency (for example, log ratio < -0.8 for 50% or more probes in a probe set) is recommended for this mutant.

ISSN: 1471-2164