diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql
index a89cd1f50..7ab8394a5 100644
--- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql
+++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage.sql
@@ -1,20 +1,7 @@
-/*
- * Copyright (c) 2012 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+PARAMETERS(AnalysisId INTEGER)
+
 select
-  (CAST(a.analysis_id as varchar) || '<>' || a.lineages) as key,
+  (CAST(AnalysisId as varchar) || '<>' || a.lineages) as key,
   a.analysis_id,
   a.lineages,
   max(a.totalLineages) as totalLineages,
@@ -25,13 +12,13 @@ select
   round(100 * (cast(sum(a.total) as float) / cast(max(a.total_reads) as float)), 2) as percent,
   group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele,
 
-  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as integer) as total_reads_from_locus,
 
-  round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  round(100 * (cast(sum(a.total) as float) / cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as float)), 2) as percent_from_locus,
   group_concat(distinct a.rowid, ',') as rowids
@@ -47,15 +34,16 @@ FROM (
     group_concat(distinct coalesce(j.ref_nt_id.locus, j.ref_nt_id.name), chr(10)) as loci,
 
     total,
-    cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id) as integer) as total_reads,
+    cast((select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as integer) as total_reads,
     group_concat(distinct hs.haplotype, chr(10)) as haplotypesWithAllele
 
   from sequenceanalysis.alignment_summary a
-  join sequenceanalysis.alignment_summary_junction j ON (j.alignment_id = a.rowid and j.status = true)
+  join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true)
   left join sequenceanalysis.haplotype_sequences hs ON ((
     (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR
     (hs.name = j.ref_nt_id.name AND hs.type = 'Allele')
   ) AND hs.haplotype.datedisabled IS NULL)
+  WHERE a.analysis_id = AnalysisId
   group by a.analysis_id, a.rowid, a.total
 
 ) a
diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.query.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.query.xml
deleted file mode 100644
index 2876baf89..000000000
--- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.query.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<query xmlns="http://labkey.org/data/xml/query">
-    <metadata>
-        <tables xmlns="http://labkey.org/data/xml">
-            <table tableName="alignment_summary_by_lineage_pivoted" tableDbType="TABLE">
-                <tableTitle>Alignment Summary By Lineage</tableTitle>
-            </table>
-        </tables>
-    </metadata>
-</query>
diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.sql
deleted file mode 100644
index 13bb7d346..000000000
--- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_by_lineage_pivoted.sql
+++ /dev/null
@@ -1,9 +0,0 @@
-SELECT
-  a.analysis_id,
-  a.lineages,
-  sum(a.percent) as percent
-
-FROM sequenceanalysis.alignment_summary_by_lineage a
-
-GROUP BY a.analysis_id, a.lineages
-PIVOT percent BY lineages
\ No newline at end of file
diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql
index 5bfff44a0..ee61c695e 100644
--- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql
+++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.sql
@@ -1,18 +1,5 @@
-/*
- * Copyright (c) 2012 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+PARAMETERS(AnalysisId INTEGER)
+
 select
   a.analysis_id,
   a.alleles,
@@ -36,13 +23,13 @@ select
   group_concat(a.rowid, ',') as rowids,
   group_concat(distinct a.haplotypesWithAllele) as haplotypesWithAllele,
 
-  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  CAST((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as INTEGER) as total_reads_from_locus,
 
-  round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id AND s.rowid IN (
-      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.ref_nt_id.locus = a.loci and asj.status = true
+  round(100 * (cast(sum(a.total) as float) / CASE WHEN count(a.lineages) = 0 THEN max(a.total_reads) ELSE cast((select sum(s.total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId AND s.rowid IN (
+      SELECT distinct asj.alignment_id from sequenceanalysis.alignment_summary_junction asj WHERE asj.analysis_id = AnalysisId AND asj.ref_nt_id.locus = a.loci and asj.status = true
     )
   ) as float) END), 2) as percent_from_locus,
   max(lastModified) as lastModified,
@@ -67,14 +54,15 @@ FROM (
     total_forward,
     total_reverse,
     valid_pairs,
-    (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = a.analysis_id) as total_reads,
+    (select sum(total) as total FROM sequenceanalysis.alignment_summary s WHERE s.analysis_id = AnalysisId) as total_reads,
     max(j.modified) as lastModified
   from sequenceanalysis.alignment_summary a
-  left join sequenceanalysis.alignment_summary_junction j ON (j.alignment_id = a.rowid and j.status = true)
+  left join sequenceanalysis.alignment_summary_junction j ON (j.analysis_id = AnalysisId AND j.alignment_id = a.rowid and j.status = true)
   left join sequenceanalysis.haplotype_sequences hs ON ((
     (hs.name = j.ref_nt_id.lineage AND hs.type = 'Lineage') OR
     (hs.name = j.ref_nt_id.name AND hs.type = 'Allele')
   ) AND hs.haplotype.datedisabled IS NULL)
+  WHERE a.analysis_id = AnalysisId
   group by a.analysis_id, a.rowid, a.total, total_forward, total_reverse, valid_pairs
 
 ) a
diff --git a/SequenceAnalysis/resources/schemas/sequenceanalysis.xml b/SequenceAnalysis/resources/schemas/sequenceanalysis.xml
index 5e420b38c..322de8124 100644
--- a/SequenceAnalysis/resources/schemas/sequenceanalysis.xml
+++ b/SequenceAnalysis/resources/schemas/sequenceanalysis.xml
@@ -523,17 +523,8 @@
                     <onClick>SequenceAnalysis.window.RunExportWindow.downloadFilesForAnalysis(dataRegionName);</onClick>
                 </item>
                 <item text="Alignment Reports">
-                    <item text="Alignment Summary">
-                        <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'alignment_summary_grouped'})</onClick>
-                    </item>
-                    <item text="Alignment Summary, By Lineage">
-                        <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'alignment_summary_by_lineage'})</onClick>
-                    </item>
-                    <item text="Alignment Summary, Pivoted By Lineage">
-                        <onClick>SequenceAnalysis.Buttons.viewAlignmentsPivoted(dataRegionName)</onClick>
-                    </item>
                     <item text="Matching Haplotypes">
-                        <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'haplotypeMatches'})</onClick>
+                        <onClick>SequenceAnalysis.Buttons.viewMatchingHaplotypes(dataRegionName)</onClick>
                     </item>
                     <item text="View Coverage">
                         <onClick>SequenceAnalysis.Buttons.viewQuery(dataRegionName, {queryName: 'sequence_coverage'})</onClick>
diff --git a/SequenceAnalysis/resources/views/sbtToGeneTable.html b/SequenceAnalysis/resources/views/sbtToGeneTable.html
deleted file mode 100644
index f506f9472..000000000
--- a/SequenceAnalysis/resources/views/sbtToGeneTable.html
+++ /dev/null
@@ -1,454 +0,0 @@
-<script type="text/javascript" nonce="<%=scriptNonce%>">
-    Ext4.onReady(function(){
-        //TODO: account for features duplicated across genomes?
-        Ext4.define('SequenceAnalysis.panel.SBTExportPanel', {
-            extend: 'Ext.panel.Panel',
-            initComponent: function () {
-                Ext4.apply(this, {
-                    border: false,
-                    bodyStyle: 'padding: 5px;',
-                    items: [{
-                        xtype: 'ldk-simplecombo',
-                        fieldLabel: 'Header Type',
-                        storeValues: ['ReadsetId', 'OutputFileId'],
-                        itemId: 'headerType',
-                        value: 'ReadsetId',
-                        forceSelection: true
-                    },{
-                        xtype: 'button',
-                        text: 'Load',
-                        handler: this.loadData,
-                        scope: this
-                    },{
-                        xtype: 'checkbox',
-                        fieldLabel: 'Show Pct Instead of Reads',
-                        itemId: 'showPct'
-                    },{
-                        itemId: 'genomeValues',
-                        style: 'padding-top: 10px;padding-bottom: 10px;',
-                        border: false,
-                        defaults: {
-                            border: false
-                        }
-                    },{
-                        itemId: 'output',
-                        xtype: 'textarea',
-                        height: 300,
-                        width: 800
-                    }]
-                });
-
-                this.callParent(arguments);
-
-                Ext4.Msg.wait('Loading...');
-                this.loadTable();
-            },
-
-            loadTable: function(){
-                LABKEY.Query.selectRows({
-                    method: 'POST',
-                    containerPath: Laboratory.Utils.getQueryContainerPath(),
-                    schemaName: 'sequenceanalysis',
-                    queryName: 'outputfiles',
-                    filterArray: [LABKEY.Filter.create('rowid', this.outputFileId)],
-                    scope: this,
-                    columns: 'rowid,dataid,library_id',
-                    failure: LDK.Utils.getErrorCallback(),
-                    success: function(results){
-                        if (!results || !results.rows || !results.rows.length){
-                            Ext4.Msg.hide();
-                            Ext4.Msg.alert('Error', 'No rows found for ID: ' + this.outputFileId);
-                            return;
-                        }
-
-                        LABKEY.Ajax.request({
-                            url: LABKEY.ActionURL.buildURL('experiment', 'showFile', Laboratory.Utils.getQueryContainerPath(), {rowId: results.rows[0].dataid, inline: false}),
-                            scope: this,
-                            failure: LDK.Utils.getErrorCallback(),
-                            success: this.parseTable
-                        });
-                    }
-                })
-            },
-
-            parseTable: function(results){
-                if (!results || !results.responseText){
-                    Ext4.Msg.hide();
-                    Ext4.Msg.alert('Error', 'Unable to load gene table');
-                    return;
-                }
-
-                Ext4.Msg.hide();
-                var header = results.responseText.split('\n')[0];
-                this.headerValues = header.split('\t');
-                this.headerValues = this.headerValues.slice(4);
-
-                this.loadData();
-            },
-
-            loadData: function(){
-                var type = this.down('#headerType').getValue();
-
-                //first find readsets:
-                var queryName, queryField, columns, readsetField;
-                if (type === 'ReadsetId'){
-                    queryName = 'sequence_readsets';
-                    queryField = 'rowid';
-                    columns = 'rowid';
-                    readsetField = 'rowid';
-                }
-                else {
-                    queryName = 'outputfiles';
-                    queryField = 'rowid';
-                    columns = 'readset,rowid';
-                    readsetField = 'readset';
-                }
-
-                LABKEY.Query.selectRows({
-                    method: 'POST',
-                    containerPath: Laboratory.Utils.getQueryContainerPath(),
-                    schemaName: 'sequenceanalysis',
-                    queryName: queryName,
-                    filterArray: [LABKEY.Filter.create(queryField, this.headerValues.join(';'), LABKEY.Filter.Types.IN)],
-                    scope: this,
-                    columns: columns,
-                    failure: LDK.Utils.getErrorCallback(),
-                    success: function(results) {
-                        if (!results || !results.rows || !results.rows.length) {
-                            Ext4.Msg.hide();
-                            Ext4.Msg.alert('Error', 'No readsets found to match header line');
-                            return;
-                        }
-
-                        this.readsets = [];
-                        this.headerToReadset = {};
-                        var hasError = false;
-                        Ext4.Array.forEach(results.rows, function(r){
-                            if (r[readsetField]){
-                                this.readsets.push(r[readsetField]);
-                                this.headerToReadset[r.rowid] = [r[readsetField]];
-                            }
-                            else {
-                                Ext4.Msg.hide();
-                                Ext4.Msg.alert('Error', 'Row lacks a readset: ' + r.rowid);
-                                hasError = true;
-                                return false;
-                            }
-                        }, this);
-
-                        if (hasError){
-                            return;
-                        }
-
-                        this.queryAnalyses(this.readsets);
-                    }
-                });
-            },
-
-            queryAnalyses: function(readsets){
-                LABKEY.Query.executeSql({
-                    method: 'POST',
-                    containerPath: Laboratory.Utils.getQueryContainerPath(),
-                    schemaName: 'sequenceanalysis',
-                    sql: 'SELECT distinct a.analysis_id, a.analysis_id.readset, a.analysis_id.library_id, a.analysis_id.library_id.name FROM sequenceanalysis.alignment_summary a WHERE a.analysis_id.readset IN (' + readsets.join(',') + ')',
-                    scope: this,
-                    failure: LDK.Utils.getErrorCallback(),
-                    success: function(results) {
-                        if (!results || !results.rows || !results.rows.length) {
-                            Ext4.Msg.hide();
-                            Ext4.Msg.alert('Error', 'No analyses found for readsets');
-                            return;
-                        }
-
-                        var genomeMap = {};
-                        Ext4.Array.forEach(results.rows, function(r){
-                            genomeMap[r.library_id] = genomeMap[r.library_id] || {name: r.name, readsets: {}, analyses: []};
-                            genomeMap[r.library_id].readsets[r.readset] = genomeMap[r.library_id].readsets[r.readset] || [];
-                            genomeMap[r.library_id].readsets[r.readset].push(r.analysis_id);
-                            genomeMap[r.library_id].analyses.push(r.analysis_id);
-                        }, this);
-
-                        var toAdd = [];
-                        toAdd.push({
-                            html: 'Genome'
-                        });
-
-                        toAdd.push({
-                            html: 'Readsets'
-                        });
-
-                        toAdd.push({
-                            html: ''
-                        });
-
-                        toAdd.push({
-                            html: 'Include?'
-                        });
-
-                        toAdd.push({
-                            html: 'Min Pct'
-                        });
-
-                        toAdd.push({
-                            html: 'Report By'
-                        });
-
-                        toAdd.push({
-                            html: ''
-                        });
-
-                        for (var genomeId in genomeMap){
-                            toAdd.push({
-                                html: genomeMap[genomeId].name
-                            });
-
-                            var msgs = [];
-                            for (var rs in genomeMap[genomeId].readsets){
-                                if (genomeMap[genomeId].readsets[rs].length > 1){
-                                    msgs.push('Readset ' + rs + ' has multiple analyses for this genome (' + genomeMap[genomeId].readsets[rs].join(',') + ').  Analysis ' + genomeMap[genomeId].readsets[rs][0] + ' will be selected.')
-                                }
-                            }
-
-                            toAdd.push({
-                                html: Ext4.Object.getKeys(genomeMap[genomeId].readsets).length  + ' / ' + this.headerValues.length
-                            });
-
-                            var missing = Ext4.Array.difference(this.headerValues, Ext4.Object.getKeys(genomeMap[genomeId].readsets));
-                            if (missing.length) {
-                                toAdd.push({
-                                    xtype: 'ldk-linkbutton',
-                                    text: missing.length ? missing.length + ' missing' : '',
-                                    linkTarget: '_blank',
-                                    href: LABKEY.ActionURL.buildURL('query', 'executeQuery', Laboratory.Utils.getQueryContainerPath(), {schemaName: 'sequenceanalysis', 'query.queryName': 'sequence_readsets', 'query.rowid~in': missing.join(';')})
-                                });
-                            }
-                            else {
-                                toAdd.push({
-                                    html: ''
-                                });
-                            }
-
-                            toAdd.push({
-                                xtype: 'checkbox',
-                                checked: true,
-                                genomeId: genomeId
-                            });
-
-                            toAdd.push({
-                                xtype: 'ldk-numberfield',
-                                minValue: 0,
-                                maxValue: 100,
-                                genomeId: genomeId,
-                                value: 0
-                            });
-
-                            toAdd.push({
-                                xtype: 'ldk-simplecombo',
-                                storeValues: ['Allele', 'Lineage'],
-                                genomeId: genomeId,
-                                value: 'Allele'
-                            });
-
-                            toAdd.push({
-                                html: msgs.length ? msgs.join('<br>') : ''
-                            });
-                        }
-                        this.genomeMap = genomeMap;
-
-                        this.down('#genomeValues').removeAll();
-                        this.down('#genomeValues').add({
-                            xtype: 'form',
-                            itemId: 'genomeSelections',
-                            defaults: {
-                                border: false,
-                                style: 'padding-right: 10px;'
-                            },
-                            layout: {
-                                type: 'table',
-                                columns: 7
-                            },
-                            items: toAdd,
-                            buttonAlign: 'left',
-                            buttons: [{
-                                text: 'Load Results',
-                                scope: this,
-                                handler: this.loadResults
-                            }]
-                        });
-                    }
-                });
-            },
-
-            loadResults: function(){
-                var genomeIds = [];
-                var analysisIds = [];
-
-                //note: query everything upfront, then filter later
-                Ext4.Array.forEach(this.query('checkbox[genomeId]'), function(cb){
-                    genomeIds.push(cb.genomeId);
-                    for (var rs in this.genomeMap[cb.genomeId].readsets){
-                        analysisIds.push(this.genomeMap[cb.genomeId].readsets[rs][0]);
-                    }
-                }, this);
-                analysisIds = Ext4.unique(analysisIds);
-
-                if (!genomeIds.length){
-                    Ext4.Msg.alert('Error', 'No genomes selected');
-                    return;
-                }
-
-                Ext4.Msg.wait('Loading...');
-                if (!this.hasLoadedAlleles){
-                    var multi = new LABKEY.MultiRequest();
-
-                    multi.add(LABKEY.Query.selectRows, {
-                        method: 'POST',
-                        containerPath: Laboratory.Utils.getQueryContainerPath(),
-                        schemaName: 'sequenceanalysis',
-                        queryName: 'alignment_summary_by_lineage',
-                        columns: 'analysis_id,analysis_id/readset,analysis_id/library_id,lineages,percent,percent_from_locus,total',
-                        filterArray: [
-                            LABKEY.Filter.create('analysis_id', analysisIds.join(';'), LABKEY.Filter.Types.IN)
-                        ],
-                        scope: this,
-                        failure: LDK.Utils.getErrorCallback(),
-                        success: function(results) {
-                            if (!results || !results.rows || !results.rows.length) {
-                                return;
-                            }
-
-                            this.resultsByLineage = {};
-                            Ext4.Array.forEach(results.rows, function(r){
-                                var readset = r['analysis_id/readset'];
-                                var genomeId = r['analysis_id/library_id'];
-
-                                this.resultsByLineage[genomeId] = this.resultsByLineage[genomeId] || {};
-                                this.resultsByLineage[genomeId][readset] = this.resultsByLineage[genomeId][readset] || [];
-                                this.resultsByLineage[genomeId][readset].push(r);
-                            }, this);
-                        }
-                    });
-
-                    multi.add(LABKEY.Query.selectRows, {
-                        method: 'POST',
-                        containerPath: Laboratory.Utils.getQueryContainerPath(),
-                        schemaName: 'sequenceanalysis',
-                        queryName: 'alignment_summary_grouped',
-                        columns: 'analysis_id,analysis_id/readset,analysis_id/library_id,alleles,percent,percent_from_locus,total_reads',
-                        filterArray: [
-                            LABKEY.Filter.create('analysis_id', analysisIds.join(';'), LABKEY.Filter.Types.IN)
-                        ],
-                        scope: this,
-                        failure: LDK.Utils.getErrorCallback(),
-                        success: function(results) {
-                            if (!results || !results.rows || !results.rows.length) {
-                                return;
-                            }
-
-                            this.resultsByAllele = {};
-                            Ext4.Array.forEach(results.rows, function(r){
-                                var readset = r['analysis_id/readset'];
-                                var genomeId = r['analysis_id/library_id'];
-
-                                this.resultsByAllele[genomeId] = this.resultsByAllele[genomeId] || {};
-                                this.resultsByAllele[genomeId][readset] = this.resultsByAllele[genomeId][readset] || [];
-                                this.resultsByAllele[genomeId][readset].push(r);
-                            }, this);
-
-                        }
-                    });
-
-                    multi.send(function(){
-                        this.hasLoadedAlleles = true;
-                        this.onAlleleLoad();
-                    }, this);
-                }
-                else {
-                    this.onAlleleLoad();
-                }
-            },
-
-            onAlleleLoad: function(){
-                var output = [];
-                output.push(['GeneId', 'GeneName', 'GeneDescription', 'SamplesWithReads'].concat(this.headerValues).join('\t'));
-                Ext4.Array.forEach(this.query('checkbox[genomeId]'), function(cb){
-                    if (!cb.getValue()){
-                        return;
-                    }
-
-                    var showPct = this.down('#showPct').getValue();
-                    var type = this.query('ldk-simplecombo[genomeId=' + cb.genomeId + ']')[0].getValue();
-                    var data = type === 'Allele' ? this.resultsByAllele[cb.genomeId] : this.resultsByLineage[cb.genomeId];
-                    var pctField = type === 'Allele' ? 'percent_from_locus' : 'percent_from_locus';
-                    var featureField = type === 'Allele' ? 'alleles' : 'lineages';
-                    var totalField = type === 'Allele' ? 'total_reads' : 'total';
-                    var threshold = this.query('ldk-numberfield[genomeId=' + cb.genomeId + ']')[0].getValue();
-
-                    var allPassingFeatures = [];
-                    var dataByReadset = {};
-                    Ext4.Array.forEach(this.readsets, function(readsetId){
-                        dataByReadset[readsetId] = dataByReadset[readsetId] || {};
-                        if (data[readsetId] && !Ext4.isEmpty(data[readsetId])){
-                            Ext4.Array.forEach(data[readsetId], function(r){
-                                if (threshold){
-                                    var pct = r[pctField];
-                                    if (pct < threshold){
-                                        return;
-                                    }
-                                }
-
-                                var name = r[featureField];
-                                if (Ext4.isArray(name)){
-                                    name = name.join(',');
-                                }
-
-                                if (!name){
-                                    return;
-                                }
-
-                                name = name.replace(/\s+/g, ',');
-
-                                allPassingFeatures.push(name);
-
-                                if (dataByReadset[readsetId][name]) {
-                                    console.error('Already present: ' + readsetId + '/' + name + '/' + dataByReadset[readsetId][name]);
-                                }
-
-                                dataByReadset[readsetId][name] = showPct ? r[pctField] : r[totalField];
-                            }, this);
-                        }
-                    }, this);
-
-                    allPassingFeatures = Ext4.unique(allPassingFeatures);
-
-                    Ext4.Array.forEach(allPassingFeatures, function(name){
-                        var row = [name, '', '', ''];
-                        var samplesWithReads = 0;
-                        Ext4.Array.forEach(this.headerValues, function(hv){
-                            var readsetId = this.headerToReadset[hv];
-                            row.push(dataByReadset[readsetId][name] || 0);
-                            if (dataByReadset[readsetId][name]){
-                                samplesWithReads++;
-                            }
-                        }, this);
-                        row[3] = samplesWithReads;
-                        output.push(row.join('\t'));
-                    }, this);
-                }, this);
-
-                this.down('textarea').setValue(output.join('\n'));
-                Ext4.Msg.hide();
-            }
-        });
-
-        var webpart = <%=webpartContext%>;
-        var rowId = LABKEY.ActionURL.getParameter('outputFileId');
-        if (!rowId){
-            alert('Must Provide Output File Id');
-            return;
-        }
-        Ext4.create('SequenceAnalysis.panel.SBTExportPanel', {
-            outputFileId: rowId
-        }).render(webpart.wrapperDivId);
-    });
-</script>
\ No newline at end of file
diff --git a/SequenceAnalysis/resources/views/sbtToGeneTable.view.xml b/SequenceAnalysis/resources/views/sbtToGeneTable.view.xml
deleted file mode 100644
index e95eaf46b..000000000
--- a/SequenceAnalysis/resources/views/sbtToGeneTable.view.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<view xmlns="http://labkey.org/data/xml/view" title="Export SBT Data For Gene Counts">
-    <dependencies>
-        <dependency path="laboratory.context"/>
-        <dependency path="SequenceAnalysis/sequenceAnalysis"/>
-    </dependencies>
-</view>
\ No newline at end of file
diff --git a/SequenceAnalysis/resources/web/SequenceAnalysis/sequenceanalysisButtons.js b/SequenceAnalysis/resources/web/SequenceAnalysis/sequenceanalysisButtons.js
index e2cd084f9..df68e755c 100644
--- a/SequenceAnalysis/resources/web/SequenceAnalysis/sequenceanalysisButtons.js
+++ b/SequenceAnalysis/resources/web/SequenceAnalysis/sequenceanalysisButtons.js
@@ -163,7 +163,7 @@ SequenceAnalysis.Buttons = new function(){
             );
         },
 
-        viewAlignmentsPivoted: function(dataRegionName){
+        viewMatchingHaplotypes: function(dataRegionName){
             var dataRegion = LABKEY.DataRegions[dataRegionName];
             var checked = dataRegion.getChecked();
             if (!checked.length){
@@ -171,11 +171,16 @@ SequenceAnalysis.Buttons = new function(){
                 return;
             }
 
+            if (checked.length !== 1) {
+                alert('Only one row at a time can be selected');
+                return;
+            }
+
             window.location = LABKEY.ActionURL.buildURL(
                     'sequenceanalysis',
-                    'lineagePivot',
+                    'haplotypeMatches',
                     dataRegion.containerPath,
-                    {analysisIds: checked.join(';')}
+                    {'query.param.AnalysisId': checked[0]}
             );
         },
 
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java
index 3fc642130..e6ddc71b3 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java
@@ -57,7 +57,6 @@
 import org.labkey.sequenceanalysis.analysis.PrintReadBackedHaplotypesHandler;
 import org.labkey.sequenceanalysis.analysis.RecalculateSequenceMetricsHandler;
 import org.labkey.sequenceanalysis.analysis.RnaSeqcHandler;
-import org.labkey.sequenceanalysis.analysis.SbtGeneCountHandler;
 import org.labkey.sequenceanalysis.analysis.UnmappedSequenceBasedGenotypeHandler;
 import org.labkey.sequenceanalysis.analysis.UpdateReadsetFilesHandler;
 import org.labkey.sequenceanalysis.button.AddSraRunButton;
@@ -189,7 +188,6 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.Set;
 
@@ -389,7 +387,6 @@ public static void registerPipelineSteps()
         SequenceAnalysisService.get().registerFileHandler(new RnaSeqcHandler());
         SequenceAnalysisService.get().registerFileHandler(new CombineStarGeneCountsHandler());
         SequenceAnalysisService.get().registerFileHandler(new CombineSubreadGeneCountsHandler());
-        SequenceAnalysisService.get().registerFileHandler(new SbtGeneCountHandler());
         SequenceAnalysisService.get().registerFileHandler(new ProcessVariantsHandler());
         SequenceAnalysisService.get().registerFileHandler(new UnmappedReadExportHandler());
         SequenceAnalysisService.get().registerFileHandler(new MergeVcfsAndGenotypesHandler());
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java
deleted file mode 100644
index 0ebe5e999..000000000
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/SbtGeneCountHandler.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package org.labkey.sequenceanalysis.analysis;
-
-import org.json.JSONObject;
-import org.labkey.api.data.Container;
-import org.labkey.api.module.Module;
-import org.labkey.api.module.ModuleLoader;
-import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.PipelineJobException;
-import org.labkey.api.pipeline.RecordedAction;
-import org.labkey.api.query.DetailsURL;
-import org.labkey.api.security.User;
-import org.labkey.api.sequenceanalysis.SequenceOutputFile;
-import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
-import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
-import org.labkey.api.util.FileType;
-import org.labkey.api.view.ActionURL;
-import org.labkey.sequenceanalysis.SequenceAnalysisModule;
-
-import java.io.File;
-import java.util.LinkedHashSet;
-import java.util.List;
-
-public class SbtGeneCountHandler implements SequenceOutputHandler<SequenceOutputHandler.SequenceOutputProcessor>
-{
-    private final FileType _txtType = new FileType(List.of(".txt"), ".txt", false, FileType.gzSupportLevel.NO_GZ);
-
-    public SbtGeneCountHandler()
-    {
-
-    }
-
-    @Override
-    public String getName()
-    {
-        return "Append SBT To Gene Counts";
-    }
-
-    @Override
-    public String getDescription()
-    {
-        return "This will gather SBT data associated with the readsets used to make this combined gene table, and output them as a table suitable to append or analyze in concert with this table.";
-    }
-
-    @Override
-    public String getButtonJSHandler()
-    {
-        return null;
-    }
-
-    @Override
-    public ActionURL getButtonSuccessUrl(Container c, User u, List<Integer> outputFileIds)
-    {
-        return DetailsURL.fromString("/sequenceanalysis/sbtToGeneTable.view?outputFileId=" + outputFileIds.iterator().next(), c).getActionURL();
-    }
-
-    @Override
-    public boolean useWorkbooks()
-    {
-        return true;
-    }
-
-    @Override
-    public Module getOwningModule()
-    {
-        return ModuleLoader.getInstance().getModule(SequenceAnalysisModule.class);
-    }
-
-    @Override
-    public LinkedHashSet<String> getClientDependencies()
-    {
-        return null;
-    }
-
-    @Override
-    public boolean canProcess(SequenceOutputFile f)
-    {
-        return f.getCategory() != null && f.getCategory().startsWith("Gene Count Table") && (_txtType.isType(f.getFile()));
-    }
-
-    @Override
-    public boolean doRunRemote()
-    {
-        return false;
-    }
-
-    @Override
-    public boolean doRunLocal()
-    {
-        return false;
-    }
-
-    @Override
-    public SequenceOutputProcessor getProcessor()
-    {
-        return new Processor();
-    }
-
-    @Override
-    public boolean doSplitJobs()
-    {
-        return false;
-    }
-
-    private static class Processor implements SequenceOutputProcessor
-    {
-        @Override
-        public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
-        {
-
-        }
-
-        @Override
-        public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException
-        {
-
-        }
-    }
-}
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java
index c3d9343d7..1f7847b5f 100644
--- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java
+++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/SequenceBasedTypingAnalysis.java
@@ -177,7 +177,7 @@ public static void prepareLineageMapFiles(SequenceAnalysisJobSupport support, Lo
                 continue;
             }
 
-            File lineageMapFile = new File(sourceDirectory, genome.getGenomeId() + "_lineageMap.txt");
+            File lineageMapFile = FileUtil.appendName(sourceDirectory, genome.getGenomeId() + "_lineageMap.txt");
             try (final CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(lineageMapFile), '\t', CSVWriter.NO_QUOTE_CHARACTER))
             {
                 log.info("writing lineage map file");
@@ -227,7 +227,7 @@ public Output performAnalysisPerSampleLocal(AnalysisModel model, File inputBam,
                 throw new PipelineJobException("Genome not found: " + model.getLibraryId());
             }
 
-            File lineageMapFile = new File(getPipelineCtx().getSourceDirectory(), referenceGenome.getGenomeId() + "_lineageMap.txt");
+            File lineageMapFile = FileUtil.appendName(getPipelineCtx().getSourceDirectory(), referenceGenome.getGenomeId() + "_lineageMap.txt");
             if (lineageMapFile.exists())
             {
                 getPipelineCtx().getLogger().debug("deleting lineage map file: " + lineageMapFile.getName());
@@ -264,8 +264,8 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
             BamIterator bi = new BamIterator(inputBam, referenceGenome.getWorkingFastaFile(), getPipelineCtx().getLogger());
 
             List<AlignmentAggregator> aggregators = new ArrayList<>();
-            File workDir = new File(getPipelineCtx().getSourceDirectory(), FileUtil.getBaseName(inputBam));
-            File sbtOutputLog = new File(workDir, FileUtil.getBaseName(inputBam) + ".sbt.txt.gz");
+            File workDir = FileUtil.appendName(getPipelineCtx().getSourceDirectory(), FileUtil.getBaseName(inputBam));
+            File sbtOutputLog = FileUtil.appendName(workDir, FileUtil.getBaseName(inputBam) + ".sbt.txt.gz");
 
             SequenceBasedTypingAlignmentAggregator agg = new SequenceBasedTypingAlignmentAggregator(getPipelineCtx().getLogger(), referenceGenome.getWorkingFastaFile(), avgBaseQualityAggregator, toolParams);
             if (getProvider().getParameterByName("writeLog").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false))
@@ -277,7 +277,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
                 agg.setOutputLog(sbtOutputLog);
             }
 
-            File lineageMapFile = new File(getPipelineCtx().getSourceDirectory(), referenceGenome.getGenomeId() + "_lineageMap.txt");
+            File lineageMapFile = FileUtil.appendName(getPipelineCtx().getSourceDirectory(), referenceGenome.getGenomeId() + "_lineageMap.txt");
             if (lineageMapFile.exists())
             {
                 getPipelineCtx().getLogger().debug("using lineage map: " + lineageMapFile.getName());
@@ -371,7 +371,7 @@ public Output performAnalysisPerSampleRemote(Readset rs, File inputBam, Referenc
 
     protected File getSBTSummaryFile(File outputDir, File bam)
     {
-        return new File(outputDir, FileUtil.getBaseName(bam) + ".sbt_hits.txt.gz");
+        return FileUtil.appendName(outputDir, FileUtil.getBaseName(bam) + ".sbt_hits.txt.gz");
     }
 
     public static class AlignmentGroupCompare
@@ -383,7 +383,9 @@ public AlignmentGroupCompare(final long analysisId, Container c, User u)
         {
             this.analysisId = analysisId;
 
-            new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null).forEachResults(rs -> {
+            TableSelector ts = new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null);
+            ts.setNamedParameters(Map.of("AnalysisId", this.analysisId));
+            ts.forEachResults(rs -> {
                 if (rs.getString(FieldKey.fromString("alleles")) == null)
                 {
                     return;