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
A0 F0 I1 R1 715 38.4 1606192 96.6% 1551581 120.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,996,372 C→T *302* (TAG→TAA)  insD1 ← IS2 transposase TnpB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,996,3720CT100.0% 208.7 / NA 64*302* (TAG→TAA) insD1IS2 transposase TnpB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/38);  total (26/38)

GCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGA  >  NC_000913/2996236‑2996487
                                                                                                                                        |                                                                                                                   
gCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTta                                                                                                                   <  1:729409/139‑1 (MQ=255)
 cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTtat                                                                                                                  <  1:214691/139‑1 (MQ=255)
 cTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTtat                                                                                                                  <  1:27598/139‑1 (MQ=255)
      aaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTc                                                                                                             >  1:340234/1‑139 (MQ=255)
      aaataaTCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTACTGGATTTGCCCTTATATTTc                                                                                                             <  1:469680/139‑1 (MQ=255)
        ataatCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           <  2:75168/139‑1 (MQ=255)
        ataatCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           <  2:759855/139‑1 (MQ=255)
          aatCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGa                                                                                                         <  1:312596/139‑1 (MQ=255)
            tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACa                                                                                                       <  1:197535/139‑1 (MQ=255)
            tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACa                                                                                                       >  1:433296/1‑139 (MQ=255)
            tCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACa                                                                                                       <  1:353810/139‑1 (MQ=255)
             cccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACAt                                                                                                      <  2:340417/139‑1 (MQ=255)
              ccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATc                                                                                                     >  1:362819/1‑139 (MQ=255)
              ccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATc                                                                                                     <  2:249106/139‑1 (MQ=255)
              ccTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATc                                                                                                     <  2:271408/139‑1 (MQ=255)
                ttAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTg                                                                                                   >  2:250529/1‑139 (MQ=255)
                   gTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                <  2:149043/139‑1 (MQ=255)
                   gTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCAATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                <  1:405123/139‑1 (MQ=255)
                    tACATCAGGAACCTTATAAAAAAGCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           <  1:427052/127‑1 (MQ=255)
                    tACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           >  2:427052/1‑127 (MQ=255)
                       aTCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGa                                                                                                         <  1:329687/126‑1 (MQ=255)
                       aTCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGa                                                                                                         >  2:329687/1‑126 (MQ=255)
                        tCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACt                                                                                           >  2:299531/1‑139 (MQ=255)
                        tCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACt                                                                                           >  2:137534/1‑139 (MQ=255)
                         cAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACtt                                                                                          >  1:646678/1‑139 (MQ=255)
                           ggAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTaa                                                                                        <  2:362819/139‑1 (MQ=255)
                            gAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           <  1:799788/119‑1 (MQ=255)
                            gAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCa                                                                                                           >  2:799788/1‑119 (MQ=255)
                            gAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAAc                                                                                       <  2:13412/139‑1 (MQ=255)
                             aaCCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAAcc                                                                                      <  2:433296/139‑1 (MQ=255)
                             aaCCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAAcc                                                                                      <  2:340234/139‑1 (MQ=255)
                                  tataAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTa                                                                                 >  2:34549/1‑139 (MQ=255)
                                          aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATAttt                                                                                                              >  1:192472/1‑102 (MQ=255)
                                          aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATAttt                                                                                                              <  2:192472/102‑1 (MQ=255)
                                          aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                >  1:705190/1‑116 (MQ=255)
                                          aaCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTa                                                                                                <  2:705190/116‑1 (MQ=255)
                                           aCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                         <  2:318573/138‑1 (MQ=255)
                                           aCCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                         >  1:318573/1‑138 (MQ=255)
                                                 gTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGc                                                                  <  2:583534/139‑1 (MQ=255)
                                                     tGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGat                                                              >  1:780191/1‑139 (MQ=255)
                                                                ctcGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCC‑TTACAAGCCCGCTGCCGCAGATATTCCCGTGgcg                                                  <  1:765677/139‑1 (MQ=255)
                                                                 tcGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcg                                                  <  1:137534/139‑1 (MQ=255)
                                                                             aCAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCa                                      >  1:638150/1‑139 (MQ=255)
                                                                              cAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAg                                     <  1:299531/139‑1 (MQ=255)
                                                                               aaCCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAgc                                    >  1:129304/1‑139 (MQ=255)
                                                                                aCCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAgcg                                   <  2:302252/139‑1 (MQ=255)
                                                                                           aaCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGa                        >  2:8706/1‑139 (MQ=255)
                                                                                            aCAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAt                       >  1:424729/1‑139 (MQ=255)
                                                                                             cAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATg                      <  1:377384/139‑1 (MQ=255)
                                                                                               gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                    <  2:109435/139‑1 (MQ=255)
                                                                                               gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                    <  2:139400/139‑1 (MQ=255)
                                                                                               gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                    <  2:780191/139‑1 (MQ=255)
                                                                                               gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                    >  2:770154/1‑139 (MQ=255)
                                                                                               gATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGcc                    >  1:666435/1‑139 (MQ=255)
                                                                                                aTCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                         >  1:366886/1‑85 (MQ=255)
                                                                                                aTCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCg                                                                         <  2:366886/85‑1 (MQ=255)
                                                                                                 tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCAt                  >  2:759394/1‑139 (MQ=255)
                                                                                                 tCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCAt                  <  1:759394/139‑1 (MQ=255)
                                                                                                   aaTGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACt                                                                                           <  2:766340/64‑1 (MQ=255)
                                                                                                   aaTGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACt                                                                                           >  1:766340/1‑64 (MQ=255)
                                                                                                     tGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCAATTCGt              >  1:496836/1‑139 (MQ=255)
                                                                                                             aaTTCCAATTGTTTATTGGATTTGCCCTTATCTTTCCAGACATCTGTAATCACTTAACTCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcg                                                  <  2:508999/95‑1 (MQ=14)
                                                                                                             aaTTCCAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGgcg                                                  >  1:508999/1‑95 (MQ=255)
                                                                                                                 ccAATTGTTTATTGGATTTGCCCTTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGa  <  2:646678/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                   
GCTGATAAATAATCCCTTAGTACATCAGGAACCTTATAAAAAAACCCGCGTTCTGCAAACCTTTCTCGATAAAAGTGACAACCACTGAGTAAACAGATCAATGGAAGTAAATTCCAATTGTTTATTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGA  >  NC_000913/2996236‑2996487

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