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 F422 I52 R1 239 220.4 11079197 93.2% 10325811 100.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 619,006 A→C G251G (GGA→GGC)  fepE → regulator of length of O‑antigen component of lipopolysaccharide chains

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913619,0060AC99.0% 676.9 / ‑2.0 195G251G (GGA→GGC) fepEregulator of length of O‑antigen component of lipopolysaccharide chains
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base C (89/103);  total (90/105)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01

Only 100 of 196 total aligned reads displayed.

AAGAAAAACTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGAATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCAAACTGGAA  >  NC_000913/618909‑619102
                                                                                                 |                                                                                                
aagaaaaaCTGGCTCAGGATGGCATTAAAACGAAAAATCAACTTGATGCAAACACTCAGCGCCTCAATTCTTCACTCGACATTGCCAACGCGGCAGGCAt                                                                                                >  2:1616214/1‑100 (MQ=255)
  gaaaaaCTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTa                                                                                              <  2:5350087/100‑1 (MQ=255)
    aaaaCTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTaaa                                                                                            <  1:1490968/100‑1 (MQ=255)
        cTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGc                                                                                        >  1:1580411/1‑100 (MQ=255)
         tGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACAGTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGcc                                                                                       <  2:1238647/100‑1 (MQ=255)
         tGGCTCAGGATCGAAAAAAAACAAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGcc                                                                                       <  2:790836/100‑1 (MQ=255)
          ggCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGccc                                                                                      >  2:1002238/1‑100 (MQ=255)
            cTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGt                                                                                    >  2:3252724/1‑100 (MQ=255)
            cTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGt                                                                                    >  1:311391/1‑100 (MQ=255)
            cTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGt                                                                                    >  2:4697747/1‑100 (MQ=255)
            cTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGt                                                                                    >  2:4778294/1‑100 (MQ=255)
             tCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGtt                                                                                   >  2:521716/1‑100 (MQ=255)
              cAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCCCTCGACATTGCCAACGCGGCAGGCCTTAAAAAGCCCGttt                                                                                  >  2:3294984/1‑100 (MQ=255)
              cAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGttt                                                                                  <  2:4053602/100‑1 (MQ=255)
              cAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGttt                                                                                  >  2:2686765/1‑100 (MQ=255)
                taaTCGCATTAAAACGCAAAATCACCTAGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTAc                                                                                <  2:403038/98‑1 (MQ=255)
                ggATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTAc                                                                                <  1:450045/100‑1 (MQ=255)
                ggATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTAc                                                                                >  1:5500697/1‑100 (MQ=255)
                 gATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACa                                                                               >  1:776604/1‑100 (MQ=255)
                  aTCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAg                                                                              <  1:4758352/100‑1 (MQ=255)
                    cGCATTAAAACGAGAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTa                                                                            <  2:4982723/100‑1 (MQ=255)
                    cGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCCACGCGGCAGGCATTAAAAAGCCCGTTTACAGTa                                                                            >  2:4362780/1‑100 (MQ=255)
                     gCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTaa                                                                           >  2:2039415/1‑100 (MQ=255)
                      cATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAAt                                                                          >  1:2651200/1‑100 (MQ=255)
                       aTTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATg                                                                         <  2:1449592/100‑1 (MQ=255)
                       aTTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATg                                                                         >  2:348723/1‑100 (MQ=255)
                       aTTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATg                                                                         <  1:4256126/100‑1 (MQ=255)
                       aTTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATg                                                                         <  1:3747547/100‑1 (MQ=255)
                        ttAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATgg                                                                        >  1:1046428/1‑100 (MQ=255)
                        ttAAAACGAAAAAACAACTTGATGCAAAGATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATgg                                                                        >  1:4902754/1‑100 (MQ=255)
                          aaaaCGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTc                                                                      >  2:564712/1‑100 (MQ=255)
                          aaaaCGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTc                                                                      <  1:2211412/100‑1 (MQ=255)
                            aaCGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAg                                                                    <  2:3976589/100‑1 (MQ=255)
                             aCGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAgg                                                                   >  2:1067547/1‑100 (MQ=255)
                             aCGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAgg                                                                   >  1:879233/1‑100 (MQ=255)
                                  aaaTCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGAATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGtt                                                              <  1:4125695/100‑1 (MQ=255)
                                   aaTCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTa                                                             >  1:3890173/1‑100 (MQ=255)
                                    aTCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTaa                                                            <  1:4056352/100‑1 (MQ=255)
                                     tCAACTTGATGCAAACATTCAGCGCCTCACTTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTaaa                                                           <  1:5089675/100‑1 (MQ=255)
                                      cAACTGGAGGCAGACATTCAGCGCTTCAGTTAGTTGCTAGTCATTGCCAGCGCGGCTGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCTTTAAAg                                                          <  2:3268456/100‑1 (MQ=255)
                                       aaCTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGa                                                         <  1:460190/100‑1 (MQ=255)
                                       aaCGTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGa                                                         <  2:2340555/100‑1 (MQ=255)
                                        aCTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGAt                                                        <  2:3903608/100‑1 (MQ=255)
                                         cTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGaag                                                       >  1:4395832/1‑98 (MQ=255)
                                         cTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATg                                                       >  2:1763642/1‑100 (MQ=255)
                                          ttGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGa                                                      <  2:2107036/100‑1 (MQ=255)
                                           tGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGAc                                                     <  2:4846757/100‑1 (MQ=255)
                                               gCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCg                                                 >  2:246707/1‑100 (MQ=255)
                                                cAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGa                                                >  1:2267996/1‑100 (MQ=255)
                                                cAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGa                                                >  1:2352499/1‑100 (MQ=255)
                                                  aaCATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGAtt                                              <  2:3431593/100‑1 (MQ=255)
                                                   accttCAGCGCCTCAATTATTCACTCGCCATTGCAAACGCGGCAGGCATTCTAACGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGAttt                                             <  1:2400449/97‑1 (MQ=255)
                                                    cATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGAtttt                                            <  1:3283229/100‑1 (MQ=255)
                                                     aTTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGAttttt                                           >  1:3178834/1‑100 (MQ=255)
                                                      ttCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTc                                          <  1:2685442/100‑1 (MQ=255)
                                                        cAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTa                                        <  1:1122627/100‑1 (MQ=255)
                                                        cAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTa                                        >  1:102624/1‑100 (MQ=255)
                                                        cAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTa                                        <  1:342826/100‑1 (MQ=255)
                                                         aGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTAt                                       >  2:1047119/1‑100 (MQ=255)
                                                              cTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctc                                  <  1:1335018/100‑1 (MQ=255)
                                                              cTCAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctc                                  >  1:1896134/1‑100 (MQ=255)
                                                                cAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctctc                                >  1:2458811/1‑100 (MQ=255)
                                                                cAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctctc                                <  2:1574559/100‑1 (MQ=255)
                                                                cAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctctc                                <  1:2558318/100‑1 (MQ=255)
                                                                cAATTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTtctctc                                <  1:2299344/100‑1 (MQ=255)
                                                                 aaTTATTCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCg                               <  2:3364679/100‑1 (MQ=255)
                                                                  attattCACTCGACATTGCCAACGCGGCAGGCATTCAAAATCCCGTTTACAGTAATGGTCAGGCCGGTACAGATGACCCCGATTTTTCTATTTCTCTCgg                              >  2:2908478/1‑100 (MQ=255)
                                                                  attattCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCgg                              >  2:2191163/1‑100 (MQ=255)
                                                                   ttattCACTCGACATTTCCACCGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGt                             <  2:4161583/100‑1 (MQ=255)
                                                                   ttattCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTTTTTCGGt                             >  2:4331349/1‑100 (MQ=255)
                                                                    tattCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTg                            <  2:3833698/100‑1 (MQ=255)
                                                                     attCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGc                           <  2:5125396/100‑1 (MQ=255)
                                                                     attCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGc                           >  2:333945/1‑100 (MQ=255)
                                                                     attCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGc                           <  1:1828602/100‑1 (MQ=255)
                                                                      ttCACTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCa                          <  1:5393659/100‑1 (MQ=255)
                                                                        cACTCGACGCTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACGGTAATGGTCAGGCCGTTAAAGATGTCCCCGATTTTTCTATTTCTCTCGGGGCAGa                        <  2:1896011/100‑1 (MQ=255)
                                                                         aCTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGAc                       <  1:1303923/100‑1 (MQ=255)
                                                                          cTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACg                      >  1:5199653/1‑100 (MQ=255)
                                                                          cTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACg                      >  1:986842/1‑100 (MQ=255)
                                                                          cTCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACg                      >  2:2415496/1‑100 (MQ=255)
                                                                           tCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACgg                     <  1:2154693/100‑1 (MQ=255)
                                                                           tCGACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACgg                     <  2:1549296/100‑1 (MQ=255)
                                                                           tCGACACTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACgg                     <  1:3716825/100‑1 (MQ=255)
                                                                             gACATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTa                   <  1:344928/100‑1 (MQ=255)
                                                                               cATTGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTAtt                 >  1:2158717/1‑100 (MQ=255)
                                                                                 ttcccAACGCGTCAGGCATTAAAAAGCCCTTTTACATTAATGGTCAGTCCGTTAAAGATGACCCCGATTTGTCTATTTCTCTCGGTGCAGACGGTAttta               <  2:5441053/97‑3 (MQ=255)
                                                                                 ttGCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGa               >  2:3034821/1‑100 (MQ=255)
                                                                                   gCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAAc             <  2:3636918/100‑1 (MQ=255)
                                                                                   gCCAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAAc             <  1:3373/100‑1 (MQ=255)
                                                                                   gCCAACGCGGCAGGCAGTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAAc             >  2:5326213/1‑100 (MQ=255)
                                                                                    ccAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACg            >  2:2525668/1‑100 (MQ=255)
                                                                                    ccAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACg            <  1:2061412/100‑1 (MQ=255)
                                                                                    ccAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACg            <  2:4087834/100‑1 (MQ=255)
                                                                                    ccAACGCGGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACg            <  1:939079/100‑1 (MQ=255)
                                                                                      aaCGCGGCGGGTATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCa          <  2:2669607/100‑1 (MQ=255)
                                                                                        cgcgGCAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCaac        >  2:1809903/1‑99 (MQ=255)
                                                                                             cAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCAAACTGGa   <  1:5253341/100‑1 (MQ=255)
                                                                                             cAGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCAAACTGGa   <  1:4028337/100‑1 (MQ=255)
                                                                                              aGGCATTCAAAAGCCCTTTCAAAGTAACGGTCAGGACGTGGAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCCAACTGGaa  <  2:5453292/100‑1 (MQ=255)
                                                                                              aGGCATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGTCCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCAAACTGGaa  <  2:683760/100‑1 (MQ=255)
                                                                                                 |                                                                                                
AAGAAAAACTGGCTCAGGATCGCATTAAAACGAAAAATCAACTTGATGCAAACATTCAGCGCCTCAATTATTCACTCGACATTGCCAACGCGGCAGGAATTAAAAAGCCCGTTTACAGTAATGGTCAGGCCGTTAAAGATGACCCCGATTTTTCTATTTCTCTCGGTGCAGACGGTATTGAACGCAAACTGGAA  >  NC_000913/618909‑619102

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A