Table 1. Ten candidate mutations called by GATK (i.e., sites having a read pattern consistent with a genuine single nucleotide or indel mutation) and one confirmed deletion mutation (X 2,693,102) called only by Pindel.

				Read depth			Read depth in mutant individual
Location	Detected by GATK (G) or Pindel (P)	Mutation event	Offspring code	Female parent	Male parent	Offspring mean	Wild-type base	Mutant base	Confirmed
2L 2,301,848	G	A→C	90	28	39	50.4	30	11	Yes
2L 5,955,655	G	C→T	88	42	47	33.0	15	16	Yes
2L 19,399,106	G	G→T, A (two individuals)	74, 88	23	36	13.8	10, 4	11, 8	Yes
2R 6,136,602	G	G→A	89	33	35	61.3	21	24	Yes
2R 14,887,552	G	C→A	84	39	32	64.5	45	9	No
2R 16,372,704	G	C→T	89	26	27	49.4	32	17	Yes
3L 10,514,561	G, P	Deletion TAAAAATGCTCT	94	32	17	52.2	16	14	Yes
3R 1,431,265	G	C→T	89	32	34	44.8	33	6	Yes
3R 7,755,276	G	G→A	79	26	56	55.3	50	20	No
3R 1,2126,610	G, P	Deletion TCTCCGAAATAGG	84	28	34	48.7	22	15	Yes
X 2,693,102	P	Deletion TGTT	94	34	21	59.3	39	12	Yes

GATK, Genome Analysis Toolkit.