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 884 257.2 12958910 96.9% 12557183 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,957,548 1 bp→GG intergenic (‑117/‑744) ppiC ← / → rep peptidyl‑prolyl cis‑trans isomerase C/rep helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,957,5471.G92.5% 510.9 / 33.6 160intergenic (‑116/‑745)ppiC/reppeptidyl‑prolyl cis‑trans isomerase C/rep helicase
Reads supporting (aligned to +/- strand):  ref base . (10/2);  new base G (75/73);  total (85/75)
Fisher's exact test for biased strand distribution p-value = 3.59e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-03
*NC_0009133,957,5480TG99.4% 545.9 / NA 160intergenic (‑117/‑744)ppiC/reppeptidyl‑prolyl cis‑trans isomerase C/rep helicase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base G (85/74);  minor base C (0/1);  total (85/75)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 163 total aligned reads displayed.

AGCATGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑T‑G‑‑C‑TCGCAGG‑T‑CCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTG  >  NC_000913/3957471‑3957626
                                                                              |||                                                                                  
aGCATGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑T‑ccc                                                                   <  1:4084224/93‑2 (MQ=255)
   aTGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑T‑ccctca                                                                >  2:5770856/1‑89 (MQ=255)
   aTGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑T‑ccctca                                                                >  1:5068426/1‑89 (MQ=255)
   aTGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGGACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑T‑ccctca                                                                >  2:779203/1‑89 (MQ=255)
     taTCCGCAGATGCTAACTTAATTGTCAGTCAGGGAGTGGCTGATACATATATGGAAAAAGCCCGAAAAATCCGC‑G‑‑CTTCGCAGG‑TCCCTCAAg                                                               <  2:3470757/92‑1 (MQ=255)
      aTCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAgg                                                              >  1:4166514/1‑93 (MQ=255)
       tCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAggg                                                             <  2:397218/93‑1 (MQ=255)
        ccGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAgggg                                                            <  1:6026670/93‑1 (MQ=255)
         cGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGga                                                           <  2:2136648/93‑1 (MQ=255)
         cGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGga                                                           <  1:775692/93‑1 (MQ=255)
           cAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGgaga                                                         <  1:3892346/93‑1 (MQ=255)
            aGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGgagga                                                        >  2:2445627/1‑91 (MQ=255)
            aGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGaa                                                        >  1:5111037/1‑93 (MQ=255)
            aGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGACCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCCAGGGgagga                                                        >  2:2604226/1‑91 (MQ=255)
            aGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGGACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAggggggga                                                        >  2:1538530/1‑89 (MQ=255)
             gATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGaaa                                                       >  1:4393914/1‑93 (MQ=255)
             gATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGGACATATATTGGAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGGAC‑CCTCAAGGGGAGaaa                                                       >  1:1166106/1‑93 (MQ=255)
              aTGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGaaaa                                                      >  2:5020479/1‑93 (MQ=255)
                gCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACt                                                    >  1:3017804/1‑93 (MQ=255)
                gCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACt                                                    >  1:4294278/1‑93 (MQ=255)
                 cTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACtt                                                   >  1:1639109/1‑93 (MQ=255)
                 cTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACtt                                                   <  1:825080/93‑1 (MQ=255)
                  tAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTa                                                  <  2:2187801/93‑1 (MQ=255)
                   aaCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCCAGGGGAGGAAACTTAg                                                 >  1:514303/1‑93 (MQ=255)
                   aaCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCCAGGGGAGAAAACTTAg                                                 >  2:132061/1‑93 (MQ=255)
                   aaCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAg                                                 >  1:1849484/1‑93 (MQ=255)
                    aCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAgg                                                <  1:685222/93‑1 (MQ=255)
                    aCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAgg                                                <  2:4110545/93‑1 (MQ=255)
                    aCGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAgg                                                >  2:5331970/1‑93 (MQ=255)
                     cGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGGAAACTTAggg                                               >  1:5908735/1‑93 (MQ=255)
                     cGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAggg                                               <  2:5619305/93‑1 (MQ=255)
                       tAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCCAGGGGAGAAAACTTAGGGcc                                             >  2:1970630/1‑93 (MQ=255)
                       tAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGcc                                             >  2:4962416/1‑93 (MQ=255)
                       tAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGcc                                             <  1:3690437/93‑1 (MQ=255)
                        aaTTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCct                                            >  2:5155373/1‑93 (MQ=255)
                         aTTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCctc                                           >  2:1977139/1‑93 (MQ=255)
                         aTTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCctc                                           >  2:5200122/1‑93 (MQ=255)
                         aTTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCctc                                           <  1:3876923/93‑1 (MQ=255)
                          ttGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCctct                                          <  1:4651790/93‑1 (MQ=255)
                           tGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTa                                         >  1:3511754/1‑93 (MQ=255)
                           tGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTa                                         >  2:575637/1‑93 (MQ=255)
                            gtcagtcgGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTAt                                        <  2:3545410/93‑1 (MQ=255)
                             tcagtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATg                                       <  2:4185181/93‑1 (MQ=255)
                              cagtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATgg                                      <  1:474921/93‑1 (MQ=255)
                               agtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATggg                                     >  1:378992/1‑93 (MQ=255)
                               agtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATggg                                     >  2:2639225/1‑93 (MQ=255)
                               agtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATggg                                     >  2:6329185/1‑93 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    <  1:579687/93‑1 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    >  2:5172568/1‑93 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    >  2:5323247/1‑93 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    <  1:4103869/93‑1 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    >  2:1364245/1‑93 (MQ=255)
                                gtcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGc                                    <  1:5404287/93‑1 (MQ=255)
                                 tcagGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCt                                   <  1:3275527/93‑1 (MQ=255)
                                   agGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTAc                                 >  1:1319164/1‑93 (MQ=255)
                                   agGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTAc                                 >  2:4016867/1‑93 (MQ=255)
                                    gggAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACa                                >  2:5896571/1‑93 (MQ=255)
                                       aGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGATACAAAg                             <  2:934872/93‑1 (MQ=255)
                                       aGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAg                             >  2:5669224/1‑93 (MQ=255)
                                        gTGGCTGGTACATATATGGCAAAAGCGAGGAAAATCC‑G‑GGTT‑TCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGt                            <  1:3465299/93‑1 (MQ=255)
                                         tGGCTGGTACATATATGGCAAAAGCCCGTAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGTGCCTCTATGGGCTACAAAGTc                           <  2:3801826/93‑1 (MQ=255)
                                         tGGCTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTCCAAAGTc                           <  2:3252400/93‑1 (MQ=255)
                                         tGGCGGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTc                           <  1:2343987/93‑1 (MQ=255)
                                            cTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCAtt                        <  1:341292/93‑1 (MQ=255)
                                            cTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCAtt                        <  1:5384875/93‑1 (MQ=255)
                                            cTGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCAtt                        <  1:1915603/93‑1 (MQ=255)
                                             tGGTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTa                       >  1:6438646/1‑93 (MQ=255)
                                              ggTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTAt                      <  2:2336390/93‑1 (MQ=255)
                                              ggTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTAt                      <  1:1013719/93‑1 (MQ=255)
                                              ggTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTAt                      <  2:4715321/93‑1 (MQ=255)
                                              ggTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTAt                      >  2:3270577/1‑93 (MQ=255)
                                               gTACATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATc                     <  1:1358784/93‑1 (MQ=255)
                                                 aCATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCgg                   <  2:6035863/93‑1 (MQ=255)
                                                 aCATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCgg                   >  2:2995095/1‑93 (MQ=255)
                                                  cATATATGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCggg                  <  2:6151084/93‑1 (MQ=255)
                                                    tatatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGa                <  2:3593355/93‑1 (MQ=255)
                                                    tatatGGCAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGa                >  2:3746387/1‑93 (MQ=255)
                                                     atatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGAt               <  2:709481/93‑1 (MQ=255)
                                                     atatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGAt               <  1:4075797/93‑1 (MQ=255)
                                                     atatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGAt               >  2:572437/1‑93 (MQ=255)
                                                     atatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGAt               <  1:3039702/93‑1 (MQ=255)
                                                      tatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATg              <  1:2637307/93‑1 (MQ=255)
                                                      tatGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATg              <  1:451837/93‑1 (MQ=255)
                                                       atGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATgg             <  2:5821227/93‑1 (MQ=255)
                                                       atGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATgg             <  1:1583076/93‑1 (MQ=255)
                                                       atGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATgg             <  2:4920529/93‑1 (MQ=255)
                                                        tGGCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGt            <  2:2527709/93‑1 (MQ=255)
                                                         ggCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGtt           <  2:6299508/93‑1 (MQ=255)
                                                         ggCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGtt           >  2:3080812/1‑93 (MQ=255)
                                                          gCAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGtta          >  2:4028089/1‑93 (MQ=255)
                                                           cAAAAGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttat         >  2:1011353/1‑93 (MQ=255)
                                                           cAAAAGCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttat         >  2:644613/1‑93 (MQ=255)
                                                             aaaGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttattt       <  1:4021774/93‑1 (MQ=255)
                                                             aaaGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttattt       >  1:3665878/1‑93 (MQ=255)
                                                              aaGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttatttt      <  1:2025517/93‑1 (MQ=255)
                                                               aGCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttatttta     <  2:579905/93‑1 (MQ=255)
                                                                gCCCGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttattttat    >  1:2590033/1‑93 (MQ=255)
                                                                gCCCGGAAAATCC‑GGG‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttattttat    >  2:6025981/1‑93 (MQ=255)
                                                                 cccGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGttattttatt   <  1:428894/93‑1 (MQ=255)
                                                                  ccGGAAAATCCGG‑G‑‑CTTCGCAGG‑TCCCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTg  >  1:6126204/1‑93 (MQ=255)
                                                                              |||                                                                                  
AGCATGATCCGCAGATGCTAACGTAATTGTCAGTCAGGGAGTGGCTGGTACATATATGGCAAAAGCCCGGAAAATCC‑T‑G‑‑C‑TCGCAGG‑T‑CCTCAAGGGGAGAAAACTTAGGGCCTCTATGGGCTACAAAGTCATTATCGGGGATGGTTATTTTATTG  >  NC_000913/3957471‑3957626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A