Table 1.

Efficiency of the filtering strategy based on mutant line specificity

Line	GATK			Pindel			Number of unique mutations
	Raw output	Common variantsa	Filtered result	Raw output	Common variantsa	Filtered result
Carbon‐ion induced mutations
3‐14	1355	1330	6	10 988	10 669	3	8
3‐51	1326	1299	7	11 515	10 775	7	12
4‐13	1265	1258	3	11 048	10 681	3	6
5‐12	1190	1184	3	10 903	10 632	2	4
6‐99	1290	1256	4	2316	1918	4	8
14‐45b	21 959	1531	19 722	58 752	53 049	3890	22 115
18‐36	1298	1252	8	2319	1918	4	12
Neon‐ion induced mutations
6‐62	1356	1337	8	9396	9097	4	9
7‐30	1366	1354	2	9415	9137	3	5
7‐3B	1367	1339	8	9310	9044	8	14
Ne‐1779	1124	1111	3	9407	9213	7	10

^aVariants that were common between two or more of the mutants analyzed.

^bProbable outcrossing or seed contamination.