--- a/test-data/min_cov/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/min_cov/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,13 +1,12 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein