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
A1 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,015,976 A→G E3E (GAA→GAG)  fliJ → FliJ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,015,9760AG99.1% 346.1 / ‑5.0 111E3E (GAA→GAG) fliJFliJ
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base G (49/61);  total (49/62)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

Only 100 of 118 total aligned reads displayed.

TGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCA  >  NC_000913/2015886‑2016065
                                                                                          |                                                                                         
  aaCGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATg                                                                                       <  2:959086/93‑1 (MQ=255)
   aCGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATgg                                                                                      <  1:2786008/93‑1 (MQ=255)
   aCGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGAAGAGCATgg                                                                                      >  2:812343/1‑93 (MQ=255)
    cgcgcgGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGt                                                                                     <  2:862310/93‑1 (MQ=255)
     gcgcgGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTg                                                                                    >  1:1473116/1‑93 (MQ=255)
      cgcgGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTgc                                                                                   <  1:3491214/93‑1 (MQ=255)
      cgcgGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTgc                                                                                   <  2:1207137/93‑1 (MQ=255)
         ggACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCt                                                                                <  2:4071547/93‑1 (MQ=255)
         ggACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCt                                                                                <  1:2771251/93‑1 (MQ=255)
         ggACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGAATTTTCCCGACAGTGTCATAACCCAGGAGATAACTGCAGATGGCAGAGCATGGTGCGCt                                                                                >  2:3937722/1‑93 (MQ=255)
          gACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATTACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTg                                                                               <  2:4066266/93‑1 (MQ=255)
          gACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTg                                                                               >  2:4461027/1‑93 (MQ=255)
           aCTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTgg                                                                              <  2:3509590/93‑1 (MQ=255)
           aCTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTgg                                                                              <  2:1796357/93‑1 (MQ=255)
             tGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCCGAGCATGGTGCGCTgggg                                                                            >  2:1759511/1‑91 (MQ=255)
             tGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCg                                                                            >  2:230686/1‑93 (MQ=255)
               ggAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGAc                                                                          >  1:3502894/1‑93 (MQ=255)
                 aaGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGAccc                                                                        <  1:2106538/93‑1 (MQ=255)
                 aaGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGAccc                                                                        <  1:4206860/93‑1 (MQ=255)
                  aGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCt                                                                       <  2:3383545/93‑1 (MQ=255)
                  aGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCt                                                                       >  2:4468211/1‑93 (MQ=255)
                  aGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCt                                                                       <  2:1979370/93‑1 (MQ=255)
                  aGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCt                                                                       <  2:2563711/93‑1 (MQ=255)
                   gCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTg                                                                      <  1:675491/93‑1 (MQ=255)
                   gCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTg                                                                      <  1:2271406/93‑1 (MQ=255)
                    cGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGa                                                                     <  2:2791204/93‑1 (MQ=255)
                     gTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGaa                                                                    <  1:4151694/93‑1 (MQ=255)
                     gTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGaa                                                                    >  1:716718/1‑93 (MQ=255)
                          tcCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATc                                                               >  1:1630914/1‑93 (MQ=255)
                          tcCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATc                                                               <  2:1508939/93‑1 (MQ=255)
                          tcCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATc                                                               <  2:2486246/93‑1 (MQ=255)
                           ccAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGAGCTGGCGACCCTGAAAGATCt                                                              >  1:75008/1‑93 (MQ=255)
                              ggggCTGGATCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGc                                                           <  2:2439225/93‑1 (MQ=255)
                              ggggCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACAGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGc                                                           >  2:1730726/1‑93 (MQ=255)
                               gggCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCa                                                          <  2:1425195/93‑1 (MQ=255)
                               gggCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCa                                                          >  2:948967/1‑93 (MQ=255)
                                 gCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGa                                                        >  2:3122922/1‑93 (MQ=255)
                                     gAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGaaaaa                                                    <  2:3391935/93‑1 (MQ=255)
                                     gAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGaaaaa                                                    <  2:2415075/93‑1 (MQ=255)
                                      aGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAag                                                   >  1:4051809/1‑93 (MQ=255)
                                      aGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAag                                                   <  2:4500977/93‑1 (MQ=255)
                                        cGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAagag                                                 <  1:4129138/93‑1 (MQ=255)
                                        cGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAagag                                                 <  2:4062474/93‑1 (MQ=255)
                                         gTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAgg                                                >  2:1972990/1‑93 (MQ=255)
                                          tATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGt                                               >  1:2382400/1‑93 (MQ=255)
                                           aTTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTa                                              >  1:3449405/1‑93 (MQ=255)
                                           aTTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTa                                              >  2:2620375/1‑93 (MQ=255)
                                           aTTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTa                                              >  2:2620374/1‑93 (MQ=255)
                                           aTTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTa                                              >  1:2911266/1‑93 (MQ=255)
                                             tttCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTaga                                            <  2:2456093/93‑1 (MQ=255)
                                             tttCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTaga                                            <  1:1727094/93‑1 (MQ=255)
                                             tttCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTaga                                            <  2:533403/93‑1 (MQ=255)
                                              ttCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTagag                                           <  1:2238798/93‑1 (MQ=255)
                                               tCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAgg                                          <  2:3874859/93‑1 (MQ=255)
                                                cccGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGa                                         >  2:1289431/1‑93 (MQ=255)
                                                cccGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGa                                         <  1:2065822/93‑1 (MQ=255)
                                                 ccGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGAt                                        >  1:4050590/1‑93 (MQ=255)
                                                 ccGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGAt                                        >  1:3069573/1‑93 (MQ=255)
                                                     cAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCcg                                    <  1:816605/93‑1 (MQ=255)
                                                       gtgtCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCcgcg                                  >  2:2657116/1‑93 (MQ=255)
                                                       gtgtCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCcgcg                                  >  2:283028/1‑93 (MQ=255)
                                                          tCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCgcgcgc                               >  1:213862/1‑93 (MQ=255)
                                                           cATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGcc                              <  2:2270608/93‑1 (MQ=255)
                                                           cATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGcc                              <  1:827679/93‑1 (MQ=255)
                                                             tAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCctg                            >  2:9488/1‑93 (MQ=255)
                                                             tAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCctg                            >  2:2857376/1‑93 (MQ=255)
                                                               aCCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCctgct                          <  1:819144/93‑1 (MQ=255)
                                                                cccAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCctgctg                         >  2:3025118/1‑93 (MQ=255)
                                                                 ccAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTgg                        <  1:3855107/93‑1 (MQ=255)
                                                                  cAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTggg                       >  1:4415628/1‑93 (MQ=255)
                                                                   aGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTgggg                      >  1:4038609/1‑92 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     <  1:4416097/93‑1 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     >  2:3958982/1‑93 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     >  1:2070353/1‑93 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     >  1:2273104/1‑93 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     >  1:1013103/1‑93 (MQ=255)
                                                                    ggAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTg                     >  2:13913/1‑93 (MQ=255)
                                                                        aTAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAt                 >  1:2091204/1‑93 (MQ=255)
                                                                        aTAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAt                 >  1:933593/1‑93 (MQ=255)
                                                                        aTAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAt                 <  2:1128286/93‑1 (MQ=255)
                                                                        aTAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAt                 >  1:2677219/1‑93 (MQ=255)
                                                                         tAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATg                >  2:2655943/1‑93 (MQ=255)
                                                                         tAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATg                <  1:3140732/93‑1 (MQ=255)
                                                                          aaCGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGc               <  1:638991/93‑1 (MQ=255)
                                                                           aCGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCg              >  2:840467/1‑93 (MQ=255)
                                                                             ggCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTc            <  2:1204121/93‑1 (MQ=255)
                                                                             ggCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTc            <  2:1951587/93‑1 (MQ=255)
                                                                             ggCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTc            <  1:3607836/93‑1 (MQ=255)
                                                                             ggCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTc            <  1:2104112/93‑1 (MQ=255)
                                                                              gCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTcg           >  1:3263411/1‑93 (MQ=255)
                                                                               cAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTcgc          <  1:4029412/93‑1 (MQ=255)
                                                                                   tGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGAt      <  2:3570920/93‑1 (MQ=255)
                                                                                   tGGCAGAGCAGGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGAt      <  1:2273531/93‑1 (MQ=255)
                                                                                    ggCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATg     <  2:968878/93‑1 (MQ=255)
                                                                                     gCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGt    <  1:4142404/93‑1 (MQ=255)
                                                                                     gCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGt    <  1:1596066/93‑1 (MQ=255)
                                                                                       agagCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTca  <  2:3540751/93‑1 (MQ=255)
                                                                                       agagCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTca  >  1:3948619/1‑93 (MQ=255)
                                                                                       agagCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGACGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTca  >  1:4195201/1‑93 (MQ=255)
                                                                                       aGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTca  <  1:1754957/93‑1 (MQ=255)
                                                                                          |                                                                                         
TGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCA  >  NC_000913/2015886‑2016065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTTTGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAGCA  >  NC_000913/2015883‑2016068
                                                                                             |                                                                                            
TTTTGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAG                                                                                              >  SRR4302535.3107363/1‑94 (MQ=60)
TTTTGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAG                                                                                              <  SRR4302535.2074323/94‑1 (MQ=60)
TTTTGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAG                                                                                              <  SRR4302535.2085203/94‑1 (MQ=60)
   TGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCAT                                                                                           <  SRR4302535.4291911/94‑1 (MQ=60)
      ACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGT                                                                                        <  SRR4302535.2805836/94‑1 (MQ=60)
       CGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTG                                                                                       >  SRR4302535.1483662/1‑94 (MQ=60)
         CGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCG                                                                                     <  SRR4302535.3515476/94‑1 (MQ=60)
            GGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTG                                                                                  <  SRR4302535.2790987/94‑1 (MQ=60)
             GACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGG                                                                                 <  SRR4302535.2209055/94‑1 (MQ=60)
                 GGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGAC                                                                             >  SRR4302535.3527241/1‑94 (MQ=60)
                    AAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCT                                                                          <  SRR4302535.4235650/94‑1 (MQ=60)
                    AAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCT                                                                          <  SRR4302535.2121733/94‑1 (MQ=60)
                      GCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGA                                                                        >  SRR4302535.3187096/1‑94 (MQ=60)
                      GCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGA                                                                        <  SRR4302535.680211/94‑1 (MQ=60)
                      GCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGA                                                                        <  SRR4302535.2287603/94‑1 (MQ=60)
                       CGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAA                                                                       >  SRR4302535.721753/1‑94 (MQ=60)
                        GTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAA                                                                      <  SRR4302535.4180121/94‑1 (MQ=60)
                            CTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATC                                                                  >  SRR4302535.1642692/1‑94 (MQ=60)
                            CTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATC                                                                  <  SRR4302535.2667031/94‑1 (MQ=60)
                             TCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGAGCTGGCGACCCTGAAAGATCT                                                                 >  SRR4302535.75557/1‑94 (MQ=60)
                                AGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGC                                                              <  SRR4302535.3855452/94‑1 (MQ=60)
                                  GGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAG                                                            <  SRR4302535.1978541/94‑1 (MQ=60)
                                        GAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAG                                                      >  SRR4302535.4079547/1‑94 (MQ=60)
                                           CGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGG                                                   <  SRR4302535.4157392/94‑1 (MQ=60)
                                            GTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGT                                                  >  SRR4302535.2399508/1‑94 (MQ=60)
                                            GTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGA                                                  >  SRR4302535.812179/1‑94 (MQ=60)
                                             TATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTA                                                 >  SRR4302535.2931829/1‑94 (MQ=60)
                                             TATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTA                                                 >  SRR4302535.3473386/1‑94 (MQ=60)
                                                TTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAG                                              <  SRR4302535.1739580/94‑1 (MQ=60)
                                                 TTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGG                                             <  SRR4302535.2254725/94‑1 (MQ=60)
                                                   CCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGAT                                           >  SRR4302535.4078320/1‑94 (MQ=60)
                                                   CCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGAT                                           >  SRR4302535.3091011/1‑94 (MQ=60)
                                                   CCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGAT                                           <  SRR4302535.2080713/94‑1 (MQ=60)
                                                      GACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCC                                        <  SRR4302535.4109497/94‑1 (MQ=60)
                                                        CAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGC                                      <  SRR4302535.822331/94‑1 (MQ=60)
                                                            GTCATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGC                                  >  SRR4302535.215328/1‑94 (MQ=60)
                                                              CATAACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCT                                <  SRR4302535.833473/94‑1 (MQ=60)
                                                                  ACCCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTG                            <  SRR4302535.824893/94‑1 (MQ=60)
                                                                    CCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGG                          <  SRR4302535.3881653/94‑1 (MQ=60)
                                                                    CCAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGG                          >  SRR4302535.4445849/1‑94 (MQ=60)
                                                                     CAGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGG                         >  SRR4302535.4066256/1‑94 (MQ=60)
                                                                      AGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTG                        >  SRR4302535.1020309/1‑94 (MQ=60)
                                                                      AGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTG                        >  SRR4302535.2289320/1‑94 (MQ=60)
                                                                      AGGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTG                        >  SRR4302535.2085276/1‑94 (MQ=60)
                                                                       GGAGATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGA                       <  SRR4302535.4446323/94‑1 (MQ=60)
                                                                          GATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAT                    >  SRR4302535.2696370/1‑94 (MQ=60)
                                                                          GATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAT                    >  SRR4302535.2106274/1‑94 (MQ=60)
                                                                          GATAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAAT                    >  SRR4302535.940198/1‑94 (MQ=60)
                                                                            TAACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGC                  <  SRR4302535.3162586/94‑1 (MQ=60)
                                                                             AACGGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCG                 <  SRR4302535.643457/94‑1 (MQ=60)
                                                                                GGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCG              >  SRR4302535.3286076/1‑94 (MQ=60)
                                                                                GGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCG              <  SRR4302535.3632857/94‑1 (MQ=60)
                                                                                GGCAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCG              <  SRR4302535.2119286/94‑1 (MQ=60)
                                                                                  CAGATGGCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCG            <  SRR4302535.4056978/94‑1 (MQ=60)
                                                                                      TGGCAGAGCAGGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATG        <  SRR4302535.2289753/94‑1 (MQ=60)
                                                                                        GCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTC      <  SRR4302535.4170769/94‑1 (MQ=60)
                                                                                        GCAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTC      <  SRR4302535.1607577/94‑1 (MQ=60)
                                                                                         CAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCA     >  SRR4302535.3975576/1‑94 (MQ=60)
                                                                                         CAGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGACGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCA     >  SRR4302535.4223908/1‑94 (MQ=60)
                                                                                          AGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAG    >  SRR4302535.3725190/1‑94 (MQ=60)
                                                                                          AGAGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAG    >  SRR4302535.2249546/1‑94 (MQ=60)
                                                                                          AGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAG    <  SRR4302535.1767640/94‑1 (MQ=60)
                                                                                            AGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAGCA  <  SRR4302535.4260596/94‑1 (MQ=60)
                                                                                            AGCATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAGCA  <  SRR4302535.1122493/94‑1 (MQ=60)
                                                                                             |                                                                                            
TTTTGAACGCGCGGACTGGGAAGCGTCTCTCCAGGGGCTGGAGCGTATTTTCCCGACAGTGTCATAACCCAGGAGATAACGGCAGATGGCAGAACATGGTGCGCTGGCGACCCTGAAAGATCTGGCAGAAAAAGAGGTAGAGGATGCCGCGCGCCTGCTGGGTGAAATGCGTCGCGGATGTCAGCA  >  NC_000913/2015883‑2016068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑