diff --git a/src/backend/d3d12/ShaderModuleD3D12.cpp b/src/backend/d3d12/ShaderModuleD3D12.cpp
index ea53b12b55..7efb892df2 100644
--- a/src/backend/d3d12/ShaderModuleD3D12.cpp
+++ b/src/backend/d3d12/ShaderModuleD3D12.cpp
@@ -23,7 +23,6 @@ namespace backend { namespace d3d12 {
         spirv_cross::CompilerHLSL compiler(builder->AcquireSpirv());
 
         spirv_cross::CompilerGLSL::Options options_glsl;
-        options_glsl.vertex.flip_vert_y = false;
         options_glsl.vertex.fixup_clipspace = true;
         compiler.spirv_cross::CompilerGLSL::set_options(options_glsl);
 
diff --git a/src/backend/opengl/ShaderModuleGL.cpp b/src/backend/opengl/ShaderModuleGL.cpp
index 78ebad4c3e..a7495e1300 100644
--- a/src/backend/opengl/ShaderModuleGL.cpp
+++ b/src/backend/opengl/ShaderModuleGL.cpp
@@ -56,7 +56,6 @@ namespace backend { namespace opengl {
 #else
         options.version = 440;
 #endif
-        options.vertex.flip_vert_y = true;
         compiler.set_options(options);
 
         // Rename the push constant block to be prefixed with the shader stage type so that uniform
diff --git a/src/tests/end2end/IndexFormatTests.cpp b/src/tests/end2end/IndexFormatTests.cpp
index debf15c432..9bab9598ed 100644
--- a/src/tests/end2end/IndexFormatTests.cpp
+++ b/src/tests/end2end/IndexFormatTests.cpp
@@ -117,7 +117,7 @@ TEST_P(IndexFormatTest, Uint32) {
 
     queue.Submit(1, &commands);
 
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 100);
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 300);
 }
 
 // Test that the Uint16 index format is correctly interpreted
@@ -148,7 +148,7 @@ TEST_P(IndexFormatTest, Uint16) {
 
     queue.Submit(1, &commands);
 
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 100);
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 300);
 }
 
 // Test for primitive restart use vertices like in the drawing and draw the following
@@ -192,9 +192,9 @@ TEST_P(IndexFormatTest, Uint32PrimitiveRestart) {
 
     queue.Submit(1, &commands);
 
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 190, 210); // A
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 210, 190); // B
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 0, 0, 0), renderTarget, 210, 210); // C
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 190, 190);  // A
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 210, 210);  // B
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 0, 0, 0), renderTarget, 210, 190);      // C
 }
 
 // Test use of primitive restart with an Uint16 index format
@@ -226,9 +226,9 @@ TEST_P(IndexFormatTest, Uint16PrimitiveRestart) {
 
     queue.Submit(1, &commands);
 
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 190, 210); // A
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 210, 190); // B
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 0, 0, 0), renderTarget, 210, 210); // C
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 190, 190);  // A
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 210, 210);  // B
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 0, 0, 0), renderTarget, 210, 190);      // C
 }
 
 // Test that the index format used is the format of the last set pipeline. This is to
@@ -264,7 +264,7 @@ TEST_P(IndexFormatTest, ChangePipelineAfterSetIndexBuffer) {
 
     queue.Submit(1, &commands);
 
-    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 100);
+    EXPECT_PIXEL_RGBA8_EQ(RGBA8(0, 255, 0, 255), renderTarget, 100, 300);
 }
 
 NXT_INSTANTIATE_TEST(IndexFormatTest, MetalBackend, OpenGLBackend)
diff --git a/src/tests/end2end/InputStateTests.cpp b/src/tests/end2end/InputStateTests.cpp
index 79a4895b14..66958d29af 100644
--- a/src/tests/end2end/InputStateTests.cpp
+++ b/src/tests/end2end/InputStateTests.cpp
@@ -101,7 +101,7 @@ class InputStateTest : public NXTTest {
             // Hard code the triangle in the shader so that we don't have to add a vertex input for it.
             // Also this places the triangle in the grid based on its VertexID and InstanceID
             vs << "    const vec2 pos[3] = vec2[3](vec2(0.5f, 1.0f), vec2(0.0f, 0.0f), vec2(1.0f, 0.0f));\n";
-            vs << "    vec2 offset = vec2(float(gl_VertexIndex / 3), 3 - float(gl_InstanceIndex));\n";
+            vs << "    vec2 offset = vec2(float(gl_VertexIndex / 3), float(gl_InstanceIndex));\n";
             vs << "    vec2 worldPos = pos[gl_VertexIndex % 3] + offset;\n";
             vs << "    gl_Position = vec4(worldPos / 2 - vec2(1.0f), 0.0f, 1.0f);\n";
 
diff --git a/src/tests/end2end/PrimitiveTopologyTests.cpp b/src/tests/end2end/PrimitiveTopologyTests.cpp
index c688415d4f..bd98ea9ee4 100644
--- a/src/tests/end2end/PrimitiveTopologyTests.cpp
+++ b/src/tests/end2end/PrimitiveTopologyTests.cpp
@@ -97,6 +97,7 @@ constexpr TestLocation GetCentroid(const TestLocation& a, const TestLocation& b,
     return { (a.x + b.x + c.x) / 3, (a.y + b.y + c.y) / 3 };
 }
 
+// clang-format off
 // Offset towards one corner to avoid x or y symmetry false positives
 constexpr static unsigned int kOffset = kRTSize / 8;
 
@@ -132,13 +133,14 @@ constexpr static TestLocation kTriangleStripTestLocations[] = {
 
 constexpr static float kRTSizef = static_cast<float>(kRTSize);
 constexpr static float kVertices[] = {
-    2.f * (kPointTestLocations[0].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[0].y + 0.5f) / kRTSizef, 0.f, 1.f,
-    2.f * (kPointTestLocations[1].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[1].y + 0.5f) / kRTSizef, 0.f, 1.f,
-    2.f * (kPointTestLocations[2].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[2].y + 0.5f) / kRTSizef, 0.f, 1.f,
-    2.f * (kPointTestLocations[3].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[3].y + 0.5f) / kRTSizef, 0.f, 1.f,
-    2.f * (kPointTestLocations[4].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[4].y + 0.5f) / kRTSizef, 0.f, 1.f,
-    2.f * (kPointTestLocations[5].x + 0.5f) / kRTSizef - 1.f, 1.f - 2.f * (kPointTestLocations[5].y + 0.5f) / kRTSizef, 0.f, 1.f,
+    2.f * (kPointTestLocations[0].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[0].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
+    2.f * (kPointTestLocations[1].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[1].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
+    2.f * (kPointTestLocations[2].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[2].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
+    2.f * (kPointTestLocations[3].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[3].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
+    2.f * (kPointTestLocations[4].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[4].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
+    2.f * (kPointTestLocations[5].x + 0.5f) / kRTSizef - 1.f, 2.f * (kPointTestLocations[5].y + 0.5f) / kRTSizef - 1.0f, 0.f, 1.f,
 };
+// clang-format on
 
 class PrimitiveTopologyTest : public NXTTest {
     protected: