diff --git a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
index 967b0d0bb49..20c3d1a55d1 100644
--- a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
+++ b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
@@ -91,7 +91,7 @@ export default class BamSlightlyLazyFeature implements Feature {
     return md
   }
 
-  qualRaw(): number[] {
+  qualRaw(): Buffer | undefined {
     return this.record.qualRaw()
   }
 
diff --git a/plugins/alignments/src/BamAdapter/MismatchParser.ts b/plugins/alignments/src/BamAdapter/MismatchParser.ts
index e68ccbf9b3a..e4b2bf9628a 100644
--- a/plugins/alignments/src/BamAdapter/MismatchParser.ts
+++ b/plugins/alignments/src/BamAdapter/MismatchParser.ts
@@ -15,7 +15,7 @@ export function parseCigar(cigar: string) {
 export function cigarToMismatches(
   ops: string[],
   seq: string,
-  qual?: number[],
+  qual?: Buffer,
 ): Mismatch[] {
   let currOffset = 0
   let seqOffset = 0
@@ -97,7 +97,7 @@ export function mdToMismatches(
   cigarOps: string[],
   cigarMismatches: Mismatch[],
   seq: string,
-  qual?: number[],
+  qual?: Buffer,
 ): Mismatch[] {
   const mismatchRecords: Mismatch[] = []
   let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }
@@ -176,7 +176,8 @@ export function mdToMismatches(
         }
         const s = cigarOps ? getTemplateCoordLocal(curr.start) : curr.start
         curr.base = seq ? seq.substr(s, 1) : 'X'
-        curr.qual = qual ? qual.slice(s, s + 1)[0] : 'X'
+        const qualScore = qual?.slice(s, s + 1)[0]
+        if (qualScore) curr.qual = qualScore
         curr.altbase = token
         nextRecord()
       }
@@ -207,7 +208,7 @@ export function getMismatches(
   cigarString: string,
   mdString: string,
   seq: string,
-  qual?: number[],
+  qual?: Buffer,
 ): Mismatch[] {
   let mismatches: Mismatch[] = []
   let cigarOps: string[] = []
diff --git a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap
index 4b3e4244c06..b5d0d43c875 100644
--- a/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap
+++ b/plugins/alignments/src/BamAdapter/__snapshots__/BamAdapter.test.ts.snap
@@ -293,6 +293,7 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 40,
     "type": "mismatch",
   },
@@ -341,18 +342,21 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 216,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 222,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 228,
     "type": "mismatch",
   },
@@ -365,12 +369,14 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 235,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 241,
     "type": "mismatch",
   },
@@ -383,6 +389,7 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 248,
     "type": "mismatch",
   },
@@ -395,6 +402,7 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 255,
     "type": "mismatch",
   },
@@ -413,12 +421,14 @@ Array [
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 289,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 290,
     "type": "mismatch",
   },
@@ -431,42 +441,49 @@ Array [
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 294,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 296,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 302,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 308,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 314,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 320,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 326,
     "type": "mismatch",
   },
@@ -479,6 +496,7 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 333,
     "type": "mismatch",
   },
@@ -509,6 +527,7 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 384,
     "type": "mismatch",
   },
@@ -539,18 +558,21 @@ Array [
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 491,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 621,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 622,
     "type": "mismatch",
   },
@@ -569,24 +591,28 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 800,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 802,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 803,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 804,
     "type": "mismatch",
   },
@@ -599,18 +625,21 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 808,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 809,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 814,
     "type": "mismatch",
   },
@@ -623,6 +652,7 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 820,
     "type": "mismatch",
   },
@@ -641,12 +671,14 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 828,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 883,
     "type": "mismatch",
   },
@@ -659,30 +691,35 @@ Array [
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 896,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 926,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 930,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 933,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 935,
     "type": "mismatch",
   },
@@ -695,24 +732,28 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 1001,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 1016,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 39,
     "start": 1018,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 1034,
     "type": "mismatch",
   },
@@ -731,120 +772,140 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1074,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1078,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 1112,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1133,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 1153,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 1166,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 1390,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1408,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1456,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 1507,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 1541,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 1564,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 1771,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 2197,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 2382,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 2782,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 3115,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 3117,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 3301,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 3326,
     "type": "mismatch",
   },
@@ -857,6 +918,7 @@ Array [
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 3895,
     "type": "mismatch",
   },
@@ -869,6 +931,7 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 3979,
     "type": "mismatch",
   },
@@ -881,54 +944,63 @@ Array [
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 4672,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 4698,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 4906,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 4929,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 5117,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 5210,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 5273,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 5816,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 5819,
     "type": "mismatch",
   },
@@ -941,72 +1013,84 @@ Array [
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 5905,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 5921,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 5955,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 6067,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 6102,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 6297,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 6377,
     "type": "mismatch",
   },
   Object {
     "base": "T",
     "length": 1,
+    "qual": 93,
     "start": 6533,
     "type": "mismatch",
   },
   Object {
     "base": "A",
     "length": 1,
+    "qual": 93,
     "start": 6570,
     "type": "mismatch",
   },
   Object {
     "base": "C",
     "length": 1,
+    "qual": 93,
     "start": 6806,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 6808,
     "type": "mismatch",
   },
   Object {
     "base": "G",
     "length": 1,
+    "qual": 93,
     "start": 6855,
     "type": "mismatch",
   },
diff --git a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
index ecaad1ef3f8..a2ff28915d4 100644
--- a/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
+++ b/plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
@@ -301,6 +301,7 @@ export default class CramSlightlyLazyFeature implements Feature {
         refPos: number
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         data: any
+        pos: number
         sub: string
         ref: string
       }) => {
diff --git a/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap b/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap
index 54fe3190f63..7630307da27 100644
--- a/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap
+++ b/plugins/alignments/src/CramAdapter/__snapshots__/CramAdapter.test.ts.snap
@@ -9,7 +9,7 @@ Array [
     "flags": 16,
     "is_paired": false,
     "name": "ctgA_5060_5540_1:0:0_3:1:0_15a3",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "ATACACTGGTTCGGAGACGGTTGATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCATGAGCGGCCGCTATCCGGCGGCACGCATAATATAGTGCAAG",
@@ -35,7 +35,7 @@ Array [
     "flags": 16,
     "is_paired": false,
     "name": "ctgA_4973_5541_1:0:0_1:0:0_1569",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "TACACTGGTTCGGAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCGGCTGTCCGGCGGCACGAATAATATAGTGCAAGA",
@@ -61,7 +61,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5445_5947_3:1:0_2:0:0_2b9",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "ACTGGTTCGGAGACGGTTCATGACGGGCGCGCTATATGTCGGCATCTGCTCGCCATGAGCGGCCGCTGTCCGGCGGTACGAATAATATAGTGCAAGAAAA",
@@ -87,7 +87,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5454_5906_0:1:0_2:0:0_d8a",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "GAGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGAC",
@@ -113,7 +113,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5455_5964_2:0:0_2:0:0_23e2",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "AGACGGTTCATGACGAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGGGGCCGCTGTCCAGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACT",
@@ -139,7 +139,7 @@ Array [
     "flags": 16,
     "is_paired": false,
     "name": "ctgA_5153_5559_3:0:0_1:1:0_11ac",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "GTTCATGACGAGCGCGCTATATATCGGCATCTGCGCGCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGT",
@@ -165,7 +165,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5461_5986_1:1:0_3:0:0_200e",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "TTCATGACGAGCGCGCTATATGTCGGCATCTGCGCGCCACGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTT",
@@ -191,7 +191,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5469_5932_0:0:0_2:0:0_6f8",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "GAGCGCGCTATATGTCGGCATCTGCGCCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGA",
@@ -217,7 +217,7 @@ Array [
     "flags": 16,
     "is_paired": false,
     "name": "ctgA_5079_5594_1:0:0_2:0:0_d64",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "CCCCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACTGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATTCAAAC",
@@ -243,7 +243,7 @@ Array [
     "flags": 0,
     "is_paired": false,
     "name": "ctgA_5497_6082_1:0:0_2:0:0_b2",
-    "qual": "50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50",
+    "qual": "17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17",
     "refName": "ctgA",
     "score": 37,
     "seq": "CCATGAGCGGCCGCTGTCCGGCGGCACGAATAATATAGTGCAAGAAAAACCGAAGACTACGGTTATATATGATGGAACGGCCCTCACAGCATCCTAACAG",
diff --git a/plugins/alignments/src/PileupRenderer/PileupRenderer.ts b/plugins/alignments/src/PileupRenderer/PileupRenderer.ts
index 5bece23dc4e..08cb5a03934 100644
--- a/plugins/alignments/src/PileupRenderer/PileupRenderer.ts
+++ b/plugins/alignments/src/PileupRenderer/PileupRenderer.ts
@@ -614,7 +614,7 @@ export default class PileupRenderer extends BoxRendererType {
       sortedBy,
       highResolutionScaling = 1,
       showSoftClip,
-      colorBy = {},
+      colorBy = {} as any,
       theme: configTheme,
     } = props
     const theme = createJBrowseTheme(configTheme)