diff --git a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
index 00cabde31c..c1d2c682ad 100644
--- a/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
+++ b/src/JBrowse/View/FeatureGlyph/PairedAlignment.js
@@ -49,56 +49,57 @@ renderFeature(context, fRect) {
             const block = fRect.viewInfo.block
             const l = block.bpToX(s1)
             const r = block.bpToX(s2)
-            context.fillStyle = this.getStyle(f, 'overlapColor')
-            context.strokeStyle = this.getStyle(f, 'overlapStroke')
-            context.rect(
-                l, // left
-                fRect.rect.t,
-                r-l, // width
-                fRect.rect.h
-            )
-            context.fill();
-            context.stroke()
-            context.strokeStyle = null
-            context.fillStyle = null
-            var m1 = this._getMismatches( f.read1 );
-            var m2 = this._getMismatches( f.read2 );
-            if(!m1 && !m2) {
-                return;
-            } else {
-                var mismatches = [];
-                for(var i = 0; i < m1.length; i++) {
-                    let foundMatching = false;
-                    for(var j = 0; j < m2.length; j++) {
-                        if(x1+m1[i].start == y1+m2[j].start && s1 < x1+m1[i].start && s2 > x1+m1[i].start) {
-                            foundMatching = true
-                            mismatches.push({ start: m1[i].start, base1: m1[i].base, base2: m2[j].base, type: 'mismatch', length: 1 });
+            if(r-l > 2) {
+                context.fillStyle = this.getStyle(f, 'overlapColor')
+                context.strokeStyle = this.getStyle(f, 'overlapStroke')
+                context.rect(
+                    l, // left
+                    fRect.rect.t,
+                    r-l, // width
+                    fRect.rect.h)
+                context.fill();
+                context.stroke()
+                context.strokeStyle = null
+                context.fillStyle = null
+                var m1 = this._getMismatches( f.read1 );
+                var m2 = this._getMismatches( f.read2 );
+                if(!m1 && !m2) {
+                    return;
+                } else {
+                    var mismatches = [];
+                    for(var i = 0; i < m1.length; i++) {
+                        let foundMatching = false;
+                        for(var j = 0; j < m2.length; j++) {
+                            if(x1+m1[i].start == y1+m2[j].start && s1 < x1+m1[i].start && s2 > x1+m1[i].start) {
+                                foundMatching = true
+                                mismatches.push({ start: m1[i].start, base1: m1[i].base, base2: m2[j].base, type: 'mismatch', length: 1 });
+                            }
+                        }
+                        if(m1[i].type == 'mismatch' && s1 < x1+m1[i].start && s2 > x1+m1[i].start && !foundMatching ) {
+                            mismatches.push({ start: m1[i].start, base1: m1[i].base, base2: '-', type: 'mismatch', length: 1 });
                         }
                     }
-                    if(m1[i].type == 'mismatch' && s1 < x1+m1[i].start && s2 > x1+m1[i].start && !foundMatching ) {
-                        mismatches.push({ start: m1[i].start, base1: m1[i].base, base2: '-', type: 'mismatch', length: 1 });
+                    if(mismatches.length !== 0) {
+                        this._drawOverlappingMismatches(context, fRect, mismatches, x1)
                     }
-                }
-                if(mismatches.length !== 0) {
-                    this._drawOverlappingMismatches(context, fRect, mismatches, x1)
-                }
-                mismatches = [];
-                for(var i = 0; i < m2.length; i++) {
-                    let foundMatching = false;
-                    for(var j = 0; j < m1.length; j++) {
-                        if(x1+m1[j].start == y1+m2[i].start && s1 < y1+m2[i].start && s2 > y1+m2[i].start) {
-                            //    mismatches.push({ start: m2[i].start, base1: m2[i].base, base2: m1[j].base, type: 'mismatch', length: 1 });
-                            //    would have been found in above loop also previous iteration
-                            foundMatching = true
+                    mismatches = [];
+                    for(var i = 0; i < m2.length; i++) {
+                        let foundMatching = false;
+                        for(var j = 0; j < m1.length; j++) {
+                            if(x1+m1[j].start == y1+m2[i].start && s1 < y1+m2[i].start && s2 > y1+m2[i].start) {
+                                //    mismatches.push({ start: m2[i].start, base1: m2[i].base, base2: m1[j].base, type: 'mismatch', length: 1 });
+                                //    would have been found in above loop also previous iteration
+                                foundMatching = true
+                            }
+                        }
+                        if(m2[i].type == 'mismatch' && s1 < y1+m2[i].start && s2 > y1+m2[i].start && !foundMatching) {
+                            mismatches.push({ start: m2[i].start, base1: m2[i].base, base2: '-', type: 'mismatch', length: 1 });
                         }
                     }
-                    if(m2[i].type == 'mismatch' && s1 < y1+m2[i].start && s2 > y1+m2[i].start && !foundMatching) {
-                        mismatches.push({ start: m2[i].start, base1: m2[i].base, base2: '-', type: 'mismatch', length: 1 });
+                    if(mismatches.length !== 0) {
+                        this._drawOverlappingMismatches(context, fRect, mismatches, y1)
                     }
                 }
-                if(mismatches.length !== 0) {
-                    this._drawOverlappingMismatches(context, fRect, mismatches, y1)
-                }
             }
         }
     } else {