diff --git a/src/ska_ref.rs b/src/ska_ref.rs
index 2d101f7..f0cbaa6 100644
--- a/src/ska_ref.rs
+++ b/src/ska_ref.rs
@@ -466,17 +466,24 @@ impl RefSka {
                     );
                     seq.extend(vec![
                         b'-';
-                        self.seq[curr_chrom].len() - (next_pos + half_split_len)
+                        self.seq[curr_chrom].len() - (next_pos + half_split_len) // This shouldn't overflow
                     ]);
                     curr_chrom += 1;
                     next_pos = 0;
                 }
                 if *map_pos > next_pos {
-                    // Missing bases, if no k-mers mapped over a region
-                    seq.extend(vec![b'-'; *map_pos - next_pos - half_split_len]);
-                    seq.extend_from_slice(
-                        &self.seq[curr_chrom][(*map_pos - half_split_len)..*map_pos],
-                    );
+                    if *map_pos > next_pos + half_split_len {
+                        // Missing bases, then first flanking half of split k-mer
+                        // if no k-mers mapped over a large region
+                        seq.extend(vec![b'-'; *map_pos - next_pos - half_split_len]);
+                        seq.extend_from_slice(
+                            &self.seq[curr_chrom][(*map_pos - half_split_len)..*map_pos],
+                        );
+                    } else {
+                        // Short missing region, which can happen with fastq input
+                        // Reasonable to take bases from match
+                        seq.extend_from_slice(&self.seq[curr_chrom][next_pos..*map_pos]);
+                    }
                 }
                 next_pos = *map_pos + 1;
                 if *base == b'-' {
diff --git a/tests/fastq_input.rs b/tests/fastq_input.rs
index 6a4b857..5804fba 100644
--- a/tests/fastq_input.rs
+++ b/tests/fastq_input.rs
@@ -50,6 +50,83 @@ fn align_fastq() {
     assert_eq!(var_hash(&fastq_align_out), var_hash(&fasta_align_out));
 }
 
+// Uses perfect reads with the same fasta input as merge.skf
+#[test]
+fn map_fastq() {
+    let sandbox = TestSetup::setup();
+    let rfile_name = sandbox.create_rfile(&"test", true);
+
+    Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("build")
+        .arg("-f")
+        .arg(rfile_name)
+        .arg("-o")
+        .arg("reads")
+        .args(&["--min-count", "1", "-v", "-k", "9", "--min-qual", "2"])
+        .assert()
+        .success();
+
+    let fastq_map_out = Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("map")
+        .arg(sandbox.file_string("test_ref.fa", TestDir::Input))
+        .arg("reads.skf")
+        .output()
+        .unwrap()
+        .stdout;
+
+    Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("build")
+        .arg(sandbox.file_string("test_1.fa", TestDir::Input))
+        .arg(sandbox.file_string("test_2.fa", TestDir::Input))
+        .arg("-o")
+        .arg("assemblies")
+        .args(&["-v", "-k", "9"])
+        .assert()
+        .success();
+
+    let fasta_map_out = Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("map")
+        .arg(sandbox.file_string("test_ref.fa", TestDir::Input))
+        .arg("assemblies.skf")
+        .output()
+        .unwrap()
+        .stdout;
+
+    assert_eq!(
+        String::from_utf8(fastq_map_out),
+        String::from_utf8(fasta_map_out)
+    );
+
+    let fastq_map_out_vcf = Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("map")
+        .arg(sandbox.file_string("test_ref.fa", TestDir::Input))
+        .arg("reads.skf")
+        .args(&["-f", "vcf"])
+        .output()
+        .unwrap()
+        .stdout;
+
+    let fasta_map_out_vcf = Command::new(cargo_bin("ska"))
+        .current_dir(sandbox.get_wd())
+        .arg("map")
+        .arg(sandbox.file_string("test_ref.fa", TestDir::Input))
+        .arg("assemblies.skf")
+        .args(&["-f", "vcf"])
+        .output()
+        .unwrap()
+        .stdout;
+
+    assert_eq!(
+        String::from_utf8(fastq_map_out_vcf),
+        String::from_utf8(fasta_map_out_vcf)
+    );
+}
+
 // Add errors and low quality scores to split k-mers around
 // CACT    TTAA    C,T
 // zgrep 'TTAA.AGTG' test_1_fwd.fastq.gz