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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 578,568 G→A *154* (TAG→TAA)  rzpD → DLP12 prophage, putative murein endopeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913578,5680GA100.0% 205.4 / NA 63*154* (TAG→TAA) rzpDDLP12 prophage, putative murein endopeptidase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/33);  total (30/33)

GGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTT  >  NC_000913/578434‑578698
                                                                                                                                      |                                                                                                                                  
ggCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCt                                                                                                                                <  2:303148/139‑1 (MQ=255)
           tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                     >  2:1420831/1‑139 (MQ=255)
           tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGa                                                                                                                     >  2:614981/1‑139 (MQ=255)
                ccTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGc                                                                                                                <  2:1459760/139‑1 (MQ=255)
                 cTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCg                                                                                                                      >  2:1171699/1‑132 (MQ=255)
                 cTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCg                                                                                                                      <  1:1171699/132‑1 (MQ=255)
                   ccccccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAAc                                                                                                             <  1:1420831/139‑1 (MQ=255)
                    cccccGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACt                                                                                                            <  1:1210610/139‑1 (MQ=255)
                             ggCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGAc                                                                                                                             >  1:283458/1‑113 (MQ=255)
                             ggCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGAc                                                                                                                             <  2:283458/113‑1 (MQ=255)
                              gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGATCATATCGATGGGCAACTCa                                                                                                          >  1:928649/1‑131 (MQ=255)
                              gCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCa                                                                                                          <  2:928649/131‑1 (MQ=255)
                                 gACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTAttt                                                                                               >  1:1424244/1‑139 (MQ=255)
                                     ccGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:1245225/139‑1 (MQ=255)
                                     ccGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:1013931/139‑1 (MQ=255)
                                        cTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATACAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATc                                                                                                                       <  2:390001/108‑1 (MQ=255)
                                        cTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATACAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATc                                                                                                                       >  1:390001/1‑108 (MQ=255)
                                                gATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACAcg                                                                                >  2:699921/1‑139 (MQ=255)
                                                gATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACAcg                                                                                <  1:699921/139‑1 (MQ=255)
                                                  ttattTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACAcgcg                                                                              >  1:1095509/1‑139 (MQ=255)
                                                         aCCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  1:804282/139‑1 (MQ=255)
                                                         aCCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  1:614981/139‑1 (MQ=255)
                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           <  2:1274584/118‑1 (MQ=255)
                                                          cccTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAg                                                                                           >  1:1274584/1‑118 (MQ=255)
                                                              cAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAg                                                                  <  2:1433228/139‑1 (MQ=255)
                                                               agagagagGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       >  1:104318/1‑133 (MQ=255)
                                                               agagagagGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAg                                                                       <  2:104318/133‑1 (MQ=255)
                                                                     agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGtata                                                              <  1:58087/136‑1 (MQ=255)
                                                                     agGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGtata                                                              >  2:58087/1‑136 (MQ=255)
                                                                      ggCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     >  1:101386/1‑128 (MQ=255)
                                                                      ggCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     <  2:101386/128‑1 (MQ=255)
                                                                       gCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  <  2:98815/114‑1 (MQ=255)
                                                                       gCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  >  1:98815/1‑114 (MQ=255)
                                                                           aTCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     >  2:9745/1‑139 (MQ=255)
                                                                                  tGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGTCTaa                                                     >  2:1484858/1‑132 (MQ=255)
                                                                                  tGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     <  1:1484858/132‑1 (MQ=255)
                                                                                     aaaaaCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATaaaa                                           >  1:833292/1‑139 (MQ=255)
                                                                                     aaaaaCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATaaaa                                           >  1:1583718/1‑139 (MQ=255)
                                                                                       aaaCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        >  1:88806/1‑124 (MQ=255)
                                                                                       aaaCAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        <  2:88806/124‑1 (MQ=255)
                                                                                              tGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  <  1:9745/139‑1 (MQ=255)
                                                                                                     aaCCCAGAAGTATATTAATGAGCAGTGGAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     >  2:1044070/1‑113 (MQ=255)
                                                                                                     aaCCCAGAAGTATATTAATGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCCATTATTTTGAGCAACACACACGCGCTTCCAGCGGAGTATAAATGCCTaa                                                     <  1:1044070/113‑1 (MQ=255)
                                                                                                                      aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             >  2:1470711/1‑88 (MQ=255)
                                                                                                                      aTGAGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             <  1:1470711/88‑1 (MQ=255)
                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  >  1:1497046/1‑64 (MQ=255)
                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacaca                                                                                  <  2:1497046/64‑1 (MQ=255)
                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        >  2:1138615/1‑90 (MQ=255)
                                                                                                                         aGCAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAAATATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGcc                                                        <  1:1138615/90‑1 (MQ=255)
                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             >  2:1551816/1‑83 (MQ=255)
                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATaa                                                             <  1:1551816/83‑1 (MQ=255)
                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  >  2:552333/1‑110 (MQ=255)
                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  <  1:552333/110‑1 (MQ=255)
                                                                                                                           cAGTGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGt     <  1:1554974/139‑1 (MQ=255)
                                                                                                                              tGCAGATCAAGCTGACCATATCGATGGGCAACTCATGCAATTAGTTTGAGCAATACACACGCGCTTCCCGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATACAGCTCAGACTGTTTGCTGCATTTCTGcttt  >  1:1520835/1‑139 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                <  2:630254/45‑1 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAattatt                                                                                                >  1:630254/1‑45 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacacac                                                                                 >  2:32540/1‑60 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATacacac                                                                                 <  1:32540/60‑1 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  >  1:30066/1‑107 (MQ=255)
                                                                                                                              tGCAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAAt                                  <  2:30066/107‑1 (MQ=255)
                                                                                                                                cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     >  1:1478111/1‑70 (MQ=255)
                                                                                                                                cAGATAAAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCg                                                                     <  2:1478111/70‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                  
GGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTGCAGATAGAGCTGACCATATCGATGGGCAACTCATGCAATTATTTTGAGCAATACACACGCGCTTCCAGCGGAGTATAAATGCCTAAAGTAATAAAACCGAGCAATCCATTTACGAATGTTTGCTGGGTTTCTGTTTT  >  NC_000913/578434‑578698

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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