diff --git a/endToEndTests/test/queries/fastaAligned_multiple.json b/endToEndTests/test/queries/fastaAligned_multiple.json
index 3ec5c5b3a..ab32a139f 100644
--- a/endToEndTests/test/queries/fastaAligned_multiple.json
+++ b/endToEndTests/test/queries/fastaAligned_multiple.json
@@ -3,7 +3,10 @@
   "query": {
     "action": {
       "type": "FastaAligned",
-      "sequenceName": ["testSecondSequence", "S"]
+      "sequenceName": [
+        "testSecondSequence",
+        "S"
+      ]
     },
     "filterExpression": {
       "type": "IntBetween",
@@ -14,24 +17,24 @@
   },
   "expectedQueryResult": [
     {
-      "S": "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAI--SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV-YHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILARLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
+      "S": "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAI--SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV-YHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILARLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
       "gisaid_epi_isl": "EPI_ISL_1408408",
       "testSecondSequence": "ACGT"
     },
     {
-      "S": "MFVFLVLLPLVSSQCVNLITRTQ---SYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKXXXXXXXXXXXXXXNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNTPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
+      "S": "MFVFLVLLPLVSSQCVNLITRTQ---SYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKXXXXXXXXXXXXXXNKLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
       "gisaid_epi_isl": "EPI_ISL_1749899",
       "testSecondSequence": "AAGN"
     },
     {
-      "S": "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*",
+      "S": "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*",
       "gisaid_epi_isl": "EPI_ISL_1749892",
       "testSecondSequence": "ACGT"
     },
     {
-      "S": "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAI--SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV-YHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILARLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
+      "S": "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAI--SGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGV-YHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIDDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSHRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPINFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILARLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTHNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT*",
       "gisaid_epi_isl": "EPI_ISL_2016901",
       "testSecondSequence": "ACGT"
     }
   ]
-}
+}
\ No newline at end of file
diff --git a/include/silo/storage/aa_store.h b/include/silo/storage/aa_store.h
index 859c5f8fc..74d735eec 100644
--- a/include/silo/storage/aa_store.h
+++ b/include/silo/storage/aa_store.h
@@ -47,7 +47,7 @@ class AAPosition {
    AASymbolMap<roaring::Roaring> bitmaps;
    std::optional<AA_SYMBOL> symbol_whose_bitmap_is_flipped = std::nullopt;
 
-   void flipMostNumerousBitmap(uint32_t sequence_count);
+   std::optional<silo::AA_SYMBOL> flipMostNumerousBitmap(uint32_t sequence_count);
 };
 
 class AAStorePartition {
@@ -58,6 +58,7 @@ class AAStorePartition {
    void serialize(Archive& archive, [[maybe_unused]] const uint32_t version) {
       // clang-format off
       archive & sequence_count;
+      archive & indexing_differences_to_reference_sequence;
       archive & positions;
       archive & aa_symbol_x_bitmaps;
       // clang-format on
@@ -71,6 +72,7 @@ class AAStorePartition {
    explicit AAStorePartition(const std::vector<AA_SYMBOL>& reference_sequence);
 
    const std::vector<AA_SYMBOL>& reference_sequence;
+   std::vector<std::pair<size_t, AA_SYMBOL>> indexing_differences_to_reference_sequence;
    std::vector<AAPosition> positions;
    std::vector<roaring::Roaring> aa_symbol_x_bitmaps;
    uint32_t sequence_count = 0;
diff --git a/include/silo/storage/sequence_store.h b/include/silo/storage/sequence_store.h
index 1e3115530..8a1765d88 100644
--- a/include/silo/storage/sequence_store.h
+++ b/include/silo/storage/sequence_store.h
@@ -48,7 +48,7 @@ class NucPosition {
    NucleotideSymbolMap<roaring::Roaring> bitmaps;
    std::optional<NUCLEOTIDE_SYMBOL> symbol_whose_bitmap_is_flipped = std::nullopt;
 
-   void flipMostNumerousBitmap(uint32_t sequence_count);
+   std::optional<silo::NUCLEOTIDE_SYMBOL> flipMostNumerousBitmap(uint32_t sequence_count);
 };
 
 struct SequenceStoreInfo {
@@ -64,6 +64,7 @@ class SequenceStorePartition {
    void serialize(Archive& archive, [[maybe_unused]] const uint32_t version) {
       // clang-format off
       archive & positions;
+      archive & indexing_differences_to_reference_genome;
       archive & nucleotide_symbol_n_bitmaps;
       archive & sequence_count;
       // clang-format on
@@ -77,6 +78,7 @@ class SequenceStorePartition {
    explicit SequenceStorePartition(const std::vector<NUCLEOTIDE_SYMBOL>& reference_genome);
 
    const std::vector<NUCLEOTIDE_SYMBOL>& reference_genome;
+   std::vector<std::pair<size_t, NUCLEOTIDE_SYMBOL>> indexing_differences_to_reference_genome;
    std::vector<NucPosition> positions;
    std::vector<roaring::Roaring> nucleotide_symbol_n_bitmaps;
    uint32_t sequence_count = 0;
diff --git a/src/silo/query_engine/actions/aa_mutations.cpp b/src/silo/query_engine/actions/aa_mutations.cpp
index f8bab4c4f..c6f9bbac1 100644
--- a/src/silo/query_engine/actions/aa_mutations.cpp
+++ b/src/silo/query_engine/actions/aa_mutations.cpp
@@ -221,10 +221,9 @@ void from_json(const nlohmann::json& json, std::unique_ptr<AAMutations>& action)
       for (const auto& child : json["sequenceName"]) {
          CHECK_SILO_QUERY(
             child.is_string(),
-            "AminoAcidMutations action can have the field sequenceName of type string or an array "
-            "of "
-            "strings, but no other type; while parsing array encountered the element " +
-               child.dump() + " which is not of type string"
+            "The field sequenceName of AminoAcidMutations action must have type string or an "
+            "array, if present. Found:" +
+               child.dump()
          )
          sequence_names.emplace_back(child.get<std::string>());
       }
diff --git a/src/silo/query_engine/actions/fasta_aligned.cpp b/src/silo/query_engine/actions/fasta_aligned.cpp
index 6b53b2f2d..4ba58a635 100644
--- a/src/silo/query_engine/actions/fasta_aligned.cpp
+++ b/src/silo/query_engine/actions/fasta_aligned.cpp
@@ -43,6 +43,11 @@ std::string reconstructNucSequence(
       silo::nucleotideSymbolToChar
    );
 
+   for (const auto& [position_id, symbol] :
+        sequence_store.indexing_differences_to_reference_genome) {
+      reconstructed_sequence[position_id] = nucleotideSymbolToChar(symbol);
+   }
+
    tbb::
       parallel_for(
          tbb::blocked_range<size_t>(0, sequence_store.positions.size()),
@@ -74,6 +79,10 @@ std::string reconstructAASequence(const AAStorePartition& aa_store, uint32_t seq
       silo::aaSymbolToChar
    );
 
+   for (const auto& [position_id, symbol] : aa_store.indexing_differences_to_reference_sequence) {
+      reconstructed_sequence[position_id] = aaSymbolToChar(symbol);
+   }
+
    tbb::
       parallel_for(
          tbb::blocked_range<size_t>(0, aa_store.positions.size()),
diff --git a/src/silo/storage/aa_store.cpp b/src/silo/storage/aa_store.cpp
index 53fab4360..b12d82b23 100644
--- a/src/silo/storage/aa_store.cpp
+++ b/src/silo/storage/aa_store.cpp
@@ -21,7 +21,7 @@ silo::AAPosition::AAPosition(std::optional<AA_SYMBOL> symbol) {
    symbol_whose_bitmap_is_flipped = symbol;
 }
 
-void silo::AAPosition::flipMostNumerousBitmap(uint32_t sequence_count) {
+std::optional<silo::AA_SYMBOL> silo::AAPosition::flipMostNumerousBitmap(uint32_t sequence_count) {
    std::optional<AA_SYMBOL> previous_flipped_bitmap_symbol = symbol_whose_bitmap_is_flipped;
    std::optional<AA_SYMBOL> new_flipped_bitmap_symbol = std::nullopt;
    uint32_t max_count = 0;
@@ -50,7 +50,9 @@ void silo::AAPosition::flipMostNumerousBitmap(uint32_t sequence_count) {
          bitmaps[*new_flipped_bitmap_symbol].shrinkToFit();
       }
       symbol_whose_bitmap_is_flipped = new_flipped_bitmap_symbol;
+      return symbol_whose_bitmap_is_flipped;
    }
+   return std::nullopt;
 }
 
 silo::AAStorePartition::AAStorePartition(const std::vector<AA_SYMBOL>& reference_sequence)
diff --git a/src/silo/storage/database_partition.cpp b/src/silo/storage/database_partition.cpp
index 8baa65f1e..0bb3ca26f 100644
--- a/src/silo/storage/database_partition.cpp
+++ b/src/silo/storage/database_partition.cpp
@@ -1,5 +1,6 @@
 #include "silo/storage/database_partition.h"
 
+#include <tbb/enumerable_thread_specific.h>
 #include <tbb/parallel_for.h>
 
 #include "silo/storage/column_group.h"
@@ -22,20 +23,44 @@ DatabasePartition::DatabasePartition(std::vector<silo::preprocessing::Chunk> chu
 
 void DatabasePartition::flipBitmaps() {
    for (auto& [_, seq_store] : nuc_sequences) {
+      tbb::enumerable_thread_specific<decltype(seq_store.indexing_differences_to_reference_genome)>
+         flipped_bitmaps;
+
       auto& positions = seq_store.positions;
       tbb::parallel_for(tbb::blocked_range<uint32_t>(0, positions.size()), [&](const auto& local) {
+         auto& local_flipped_bitmaps = flipped_bitmaps.local();
          for (auto position = local.begin(); position != local.end(); ++position) {
-            positions[position].flipMostNumerousBitmap(sequence_count);
+            auto flipped_symbol = positions[position].flipMostNumerousBitmap(sequence_count);
+            if (flipped_symbol.has_value()) {
+               local_flipped_bitmaps.emplace_back(position, *flipped_symbol);
+            }
          }
       });
+      for (const auto& local : flipped_bitmaps) {
+         for (auto& element : local) {
+            seq_store.indexing_differences_to_reference_genome.emplace_back(element);
+         }
+      }
    }
-   for (auto& [_, seq_store] : aa_sequences) {
-      auto& positions = seq_store.positions;
+   for (auto& [_, aa_store] : aa_sequences) {
+      tbb::enumerable_thread_specific<decltype(aa_store.indexing_differences_to_reference_sequence)>
+         flipped_bitmaps;
+
+      auto& positions = aa_store.positions;
       tbb::parallel_for(tbb::blocked_range<uint32_t>(0, positions.size()), [&](const auto& local) {
+         auto& local_flipped_bitmaps = flipped_bitmaps.local();
          for (auto position = local.begin(); position != local.end(); ++position) {
-            positions[position].flipMostNumerousBitmap(sequence_count);
+            auto flipped_symbol = positions[position].flipMostNumerousBitmap(sequence_count);
+            if (flipped_symbol.has_value()) {
+               local_flipped_bitmaps.emplace_back(position, *flipped_symbol);
+            }
          }
       });
+      for (const auto& local : flipped_bitmaps) {
+         for (auto& element : local) {
+            aa_store.indexing_differences_to_reference_sequence.emplace_back(element);
+         }
+      }
    }
 }
 
diff --git a/src/silo/storage/sequence_store.cpp b/src/silo/storage/sequence_store.cpp
index 9c5befd9b..0c6715264 100644
--- a/src/silo/storage/sequence_store.cpp
+++ b/src/silo/storage/sequence_store.cpp
@@ -23,7 +23,9 @@ silo::NucPosition::NucPosition(std::optional<NUCLEOTIDE_SYMBOL> symbol) {
    symbol_whose_bitmap_is_flipped = symbol;
 }
 
-void silo::NucPosition::flipMostNumerousBitmap(uint32_t sequence_count) {
+std::optional<silo::NUCLEOTIDE_SYMBOL> silo::NucPosition::flipMostNumerousBitmap(
+   uint32_t sequence_count
+) {
    std::optional<NUCLEOTIDE_SYMBOL> flipped_bitmap_before = symbol_whose_bitmap_is_flipped;
    std::optional<NUCLEOTIDE_SYMBOL> max_symbol = std::nullopt;
    uint32_t max_count = 0;
@@ -51,7 +53,9 @@ void silo::NucPosition::flipMostNumerousBitmap(uint32_t sequence_count) {
          bitmaps[*max_symbol].shrinkToFit();
       }
       symbol_whose_bitmap_is_flipped = max_symbol;
+      return symbol_whose_bitmap_is_flipped;
    }
+   return std::nullopt;
 }
 
 silo::SequenceStorePartition::SequenceStorePartition(