diff --git a/tests/gdtools_apply_2/expected.gd b/tests/gdtools_apply_2/expected.gd
new file mode 100644
index 00000000..f837ca56
--- /dev/null
+++ b/tests/gdtools_apply_2/expected.gd
@@ -0,0 +1,19 @@
+#=GENOME_DIFF	1.0
+#=TITLE	input
+#=BASES-CHANGED	6
+#=BASES-DELETED	50
+#=BASES-INSERTED	883
+#=GENOME-SIZE-FINAL	47131
+#=GENOME-SIZE-INITIAL	46298
+SNP	3	.	REL606-5	1000	G	adjacent=IS1	applied_end=1000	applied_seq_id=REL606-5	applied_start=1000	within=1:1
+MOB	1	.	REL606-5	1000	IS1	-1	3	applied_end=1770	applied_seq_id=REL606-5	applied_start=999	repeat_size=768
+SNP	2	.	REL606-5	1050	T	adjacent=IS1	applied_end=1050	applied_seq_id=REL606-5	applied_start=1050	within=1
+SNP	4	.	REL606-5	1772	A	adjacent=IS1	applied_end=1772	applied_seq_id=REL606-5	applied_start=1772	within=1:2
+AMP	11	.	REL606-5	2771	50	3	applied_end=2870	applied_seq_id=REL606-5	applied_start=2771
+SNP	14	.	REL606-5	2876	T	applied_end=2776	applied_seq_id=REL606-5	applied_start=2776	before=11
+SNP	13	.	REL606-5	2881	A	applied_end=2881	applied_seq_id=REL606-5	applied_start=2881	within=11:3
+DEL	12	.	REL606-5	2896	50	applied_end=2795	applied_seq_id=REL606-5	applied_start=2795	before=11
+INS	21	.	REL606-5	3821	ATTATTATTATT	applied_end=3833	applied_seq_id=REL606-5	applied_start=3821
+SNP	22	.	REL606-5	3822	G	applied_end=3822	applied_seq_id=REL606-5	applied_start=3822	within=21:1
+MOB	23	.	REL606-5	4833	IS1	-1	3	frequency=0
+MOB	24	.	REL606-5	4834	IS1	-1	3	frequency=0.78