Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F1 I1 R1 81 47.9 2225048 94.8% 2109345 113.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,720,202 T→C S52P (TCC→CCC)  cspA → RNA chaperone and antiterminator, cold‑inducible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,720,2020TC100.0% 223.2 / NA 57S52P (TCC→CCC) cspARNA chaperone and antiterminator, cold‑inducible
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/30);  total (27/30)

TTCAACGCTGACAAAGGCTTCGGCTTCATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGTCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAA  >  NC_000913/3720082‑3720332
                                                                                                                        |                                                                                                                                  
ttCAACGCTGACAAAGGCTTCGGCTTCATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAgcg                                                                                                                  >  1:461321/1‑139 (MQ=255)
  cAACGCTGACAAAGGCTTCGGCTTCATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGCACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAgcggc                                                                                                                >  1:673130/1‑139 (MQ=255)
     cGCTGACAAAGGCTTCGGCTTCATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCt                                                                                                             <  2:910024/139‑1 (MQ=255)
                 cttcggcttcATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCa                                                                                                 <  1:278432/139‑1 (MQ=255)
                 cttcggcttcATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCa                                                                                                 <  2:728314/139‑1 (MQ=255)
                    cggcttcATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCt                                                                                              >  1:920672/1‑139 (MQ=255)
                    cggcttcATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCt                                                                                              >  1:314337/1‑139 (MQ=255)
                       cttcATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGgt                                                                                           <  1:932481/139‑1 (MQ=255)
                         tcatcaCTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGgtaa                                                                                         <  1:97944/139‑1 (MQ=255)
                                tCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:314337/139‑1 (MQ=255)
                                tCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:70381/139‑1 (MQ=255)
                                  cTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAg                                                                                <  2:461321/139‑1 (MQ=255)
                                          ggCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        <  2:217517/139‑1 (MQ=255)
                                          ggCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        <  2:411086/139‑1 (MQ=255)
                                            ctctAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCa                                                                                                                              <  2:61466/83‑1 (MQ=255)
                                            ctctAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCa                                                                                                                              >  1:61466/1‑83 (MQ=255)
                                            ctctAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTg                                                                                             >  2:862650/1‑116 (MQ=255)
                                            ctctAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTg                                                                                             <  1:862650/116‑1 (MQ=255)
                                            ctctAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAtct                                                                      >  2:517933/1‑139 (MQ=255)
                                                     tgtgTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        <  2:3409/128‑1 (MQ=255)
                                                     tgtgTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        >  1:3409/1‑128 (MQ=255)
                                                      gtgtTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAtct                                                                      >  2:138694/1‑129 (MQ=255)
                                                      gtgtTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAtct                                                                      <  1:138694/129‑1 (MQ=255)
                                                       tgtTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAg                                                           >  1:677202/1‑139 (MQ=255)
                                                       tgtTCGTACACTTCTCTGCAATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCt                                                                                              >  2:739751/1‑104 (MQ=255)
                                                       tgtTCGTACACTTCTCAGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCt                                                                                              <  1:739751/104‑1 (MQ=255)
                                                                 cTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        >  2:350674/1‑116 (MQ=255)
                                                                 cTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAAt                                                                        <  1:350674/116‑1 (MQ=255)
                                                                            tCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTg                                                                                             <  1:1097668/84‑1 (MQ=255)
                                                                            tCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTg                                                                                             >  2:1097668/1‑84 (MQ=255)
                                                                             ccAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGcc                                     <  2:673130/139‑1 (MQ=255)
                                                                              cAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCa                                    >  1:345733/1‑139 (MQ=255)
                                                                                 aaCGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCAttt                                 >  1:225417/1‑139 (MQ=255)
                                                                                   cGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  1:485837/88‑1 (MQ=255)
                                                                                   cGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  >  2:485837/1‑88 (MQ=255)
                                                                                      tGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:631068/85‑1 (MQ=255)
                                                                                      tGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  >  1:631068/1‑85 (MQ=255)
                                                                                      tGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCg                             <  2:668275/138‑1 (MQ=255)
                                                                                      tGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCg                             >  1:668275/1‑138 (MQ=255)
                                                                                        gTTACAAATCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCgggg                          >  2:528939/1‑139 (MQ=255)
                                                                                               aTCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  >  1:122056/1‑76 (MQ=255)
                                                                                               aTCTCTGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:122056/76‑1 (MQ=255)
                                                                                                  tctGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGca                                                         >  2:382575/1‑98 (MQ=255)
                                                                                                  tctGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGca                                                         <  1:382575/98‑1 (MQ=255)
                                                                                                   ctGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGAt                                            >  2:508564/1‑110 (MQ=255)
                                                                                                   ctGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGAt                                            <  1:508564/110‑1 (MQ=255)
                                                                                                    tGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAg                                                                                                                    >  2:600289/1‑37 (MQ=255)
                                                                                                    tGGACGAAGGTCAGAAAGTGCCCTTCACCATCGAAAg                                                                                                                    <  1:600289/37‑1 (MQ=255)
                                                                                                          aaGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTc        <  2:225417/139‑1 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:387041/64‑1 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  >  1:76507/1‑64 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  <  2:76507/64‑1 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAAcc                                                                                  >  1:387041/1‑64 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGca                                                         >  2:455921/1‑89 (MQ=255)
                                                                                                           aGGTCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGca                                                         <  1:455921/89‑1 (MQ=255)
                                                                                                              tCAGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGa    <  2:920672/139‑1 (MQ=255)
                                                                                                                aGAAAGTGCCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGaaa  >  2:468261/1‑139 (MQ=255)
                                                                                                                        |                                                                                                                                  
TTCAACGCTGACAAAGGCTTCGGCTTCATCACTCCTGACGATGGCTCTAAAGATGTGTTCGTACACTTCTCTGCTATCCAGAACGATGGTTACAAATCTCTGGACGAAGGTCAGAAAGTGTCCTTCACCATCGAAAGCGGCGCTAAAGGCCCGGCAGCTGGTAACGTAACCAGCCTGTAATCTCTGCTTAAAAGCACAGAATCTAAGATCCCTGCCATTTGGCGGGGATTTTTTTATTTGTTTTCAGGAAA  >  NC_000913/3720082‑3720332

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A