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 I1 R1 1357 179.3 9500450 96.1% 9129932 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,765,691 A→G V340A (GTG→GCG)  ydiJ ← putative oxidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,765,6910AG98.3% 372.1 / ‑5.0 120V340A (GTG→GCG) ydiJputative oxidase
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (59/58);  total (60/60)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 126 total aligned reads displayed.

GCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAGC  >  NC_000913/1765601‑1765780
                                                                                          |                                                                                         
gcACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGcgca                                                                                         >  2:336671/1‑93 (MQ=255)
gcACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGcgca                                                                                         >  1:4205230/1‑93 (MQ=255)
  cccgagTGCATTTCCCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATc                                                                                       <  1:3618120/90‑1 (MQ=255)
  acaGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATc                                                                                       >  1:4700514/1‑93 (MQ=255)
   caGGGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCg                                                                                      <  2:959427/93‑1 (MQ=255)
    agagTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCgg                                                                                     <  2:4119598/93‑1 (MQ=255)
    agagTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCgg                                                                                     >  2:2742352/1‑93 (MQ=255)
    agagTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCgg                                                                                     <  2:2190082/93‑1 (MQ=255)
    agagTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCgg                                                                                     >  1:3139088/1‑93 (MQ=255)
       gTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTaa                                                                                  >  2:3338258/1‑93 (MQ=255)
       gTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTaa                                                                                  <  2:173462/93‑1 (MQ=255)
           aTTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCaa                                                                              >  1:1041982/1‑93 (MQ=255)
            tttACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAAc                                                                             <  2:4279801/93‑1 (MQ=255)
            tttACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAAc                                                                             >  1:2522769/1‑93 (MQ=255)
              tACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTc                                                                           >  1:4153036/1‑93 (MQ=255)
              tACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTc                                                                           <  1:2716388/93‑1 (MQ=255)
                cccGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGc                                                                         <  1:2275155/93‑1 (MQ=255)
                cccGCTCATCAATCAGCGCCTAATCATCGCCAGCAAATTCCACAATGTGCAGCCCGAGAATCTCTTGATCAGGCGCATCGGTAATCAGCTCGc                                                                         <  2:779715/93‑1 (MQ=255)
                 ccGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCt                                                                        >  2:457420/1‑93 (MQ=255)
                 ccGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCt                                                                        <  2:4571763/93‑1 (MQ=255)
                 ccGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCt                                                                        <  1:356111/93‑1 (MQ=255)
                    cTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGAc                                                                     <  1:487457/93‑1 (MQ=255)
                    cTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGAc                                                                     >  1:2297053/1‑93 (MQ=255)
                     tcatcaATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACg                                                                    >  1:2093209/1‑93 (MQ=255)
                      catcaATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGActg                                                                   >  1:4112551/1‑91 (MQ=255)
                        tcaatcaGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGaa                                                                 <  1:3162545/93‑1 (MQ=255)
                         caatcaGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAAt                                                                <  1:1552181/93‑1 (MQ=255)
                          aatcaGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATg                                                               <  1:4109717/93‑1 (MQ=255)
                          aatcaGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATg                                                               >  2:4484070/1‑93 (MQ=255)
                           atcaGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGc                                                              >  1:1220553/1‑93 (MQ=255)
                              aGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAg                                                           <  1:2840141/93‑1 (MQ=255)
                                caccTCATCATCACCAGCAAGTTCCACAATGTTCAGCCCGATCAGCTCTTGGTCAGCCGCGTCGGTATTCAACTCGCTGACGGAATGCCAGAc                                                         <  2:1390584/91‑1 (MQ=255)
                                   cTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAat                                                      <  2:2945548/93‑1 (MQ=255)
                                    tcatcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAata                                                     >  1:1955781/1‑93 (MQ=255)
                                     catcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAatat                                                    >  2:2047749/1‑93 (MQ=255)
                                       tcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCt                                                  <  1:3046155/93‑1 (MQ=255)
                                       tcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCt                                                  >  1:1267046/1‑93 (MQ=255)
                                       tcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCt                                                  <  1:1902250/93‑1 (MQ=255)
                                       tcatcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCt                                                  <  1:3046154/93‑1 (MQ=255)
                                        catcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCtt                                                 <  1:4128849/93‑1 (MQ=255)
                                          tcaCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTcc                                               <  2:2073523/93‑1 (MQ=255)
                                            aCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCcg                                             >  1:2494760/1‑93 (MQ=255)
                                            aCCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCcg                                             <  2:1633765/93‑1 (MQ=255)
                                             ccAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCcgc                                            >  1:2124228/1‑93 (MQ=255)
                                              cAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCcgcg                                           >  1:3595350/1‑93 (MQ=255)
                                                 cAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCa                                        <  1:160951/93‑1 (MQ=255)
                                                   aaTTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGa                                      >  1:369195/1‑93 (MQ=255)
                                                    aTTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGAt                                     >  2:3877869/1‑93 (MQ=255)
                                                    aTTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGAt                                     <  1:1946517/93‑1 (MQ=255)
                                                     ttCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGAtt                                    <  1:186156/93‑1 (MQ=255)
                                                     ttCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGAtt                                    <  2:1791856/93‑1 (MQ=255)
                                                      tCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTc                                   >  2:2434266/1‑93 (MQ=255)
                                                        cacaATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAg                                 <  2:1106014/93‑1 (MQ=255)
                                                         ccaATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGc                                <  1:558316/92‑1 (MQ=255)
                                                          caATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCa                               <  2:88693/93‑1 (MQ=255)
                                                          caATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCa                               <  2:1101993/93‑1 (MQ=255)
                                                          caATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCa                               <  1:4330917/93‑1 (MQ=255)
                                                           aaTGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCAc                              >  1:123026/1‑93 (MQ=255)
                                                           aaTGTCCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCAc                              <  2:4530917/93‑1 (MQ=255)
                                                             tgtgCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACtt                            <  1:2360304/93‑1 (MQ=255)
                                                             tGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACtt                            >  2:2123315/1‑93 (MQ=255)
                                                             tGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACtt                            >  2:140455/1‑93 (MQ=255)
                                                              gTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACttt                           <  1:874737/93‑1 (MQ=255)
                                                               ttCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACtttt                          >  1:3255205/1‑93 (MQ=255)
                                                               ttCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACtttt                          >  2:2502260/1‑93 (MQ=255)
                                                                tCAGCCCGAGCATCTCTTGGTCAGGCTCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTg                         <  2:3320671/93‑1 (MQ=255)
                                                                tCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGTCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTg                         >  1:672571/1‑93 (MQ=255)
                                                                tCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTtgtg                         >  1:4653921/1‑93 (MQ=255)
                                                                tCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTg                         >  2:1758074/1‑93 (MQ=255)
                                                                tCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTg                         <  2:4275199/93‑1 (MQ=255)
                                                                 cAGCCCGAGCCTCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGa                        <  1:1086051/93‑1 (MQ=255)
                                                                  aGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAg                       >  2:1164695/1‑93 (MQ=255)
                                                                   gCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGt                      >  2:2300031/1‑93 (MQ=255)
                                                                    cccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTc                     <  2:3135989/93‑1 (MQ=255)
                                                                     ccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTcc                    >  1:1737793/1‑93 (MQ=255)
                                                                     ccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTcc                    >  1:2999379/1‑93 (MQ=255)
                                                                     ccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTcc                    >  1:2882067/1‑93 (MQ=255)
                                                                     ccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTcc                    <  2:1243694/93‑1 (MQ=255)
                                                                     ccGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTcc                    <  1:2665739/93‑1 (MQ=255)
                                                                      cGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCa                   >  1:1178796/1‑93 (MQ=255)
                                                                      cGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCa                   >  2:730817/1‑93 (MQ=255)
                                                                        aGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCAcc                 <  2:834710/93‑1 (MQ=255)
                                                                        aGCATCTCTTGGTCAGGCGCATCCGTAATCACCTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCAcc                 <  2:2587382/93‑1 (MQ=255)
                                                                         gCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCg                >  1:980670/1‑93 (MQ=255)
                                                                           aTCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGtc              >  2:944583/1‑93 (MQ=255)
                                                                           aTCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGtc              >  2:1118121/1‑93 (MQ=255)
                                                                           aTCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTAAGCACTTTTGAGTCCACCgct              >  2:1118120/1‑91 (MQ=255)
                                                                           aTCTCTTGGTCAGGCGCATAGGTAATCAAATAGCTGACGGAATGCCAGACAATATCTTCACGAGCCAGATTCAGCACTTTTGAGTCCActggc              >  2:944584/1‑89 (MQ=255)
                                                                            tctcTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGtct             >  1:1065185/1‑93 (MQ=255)
                                                                            tctcTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGtct             >  1:3454903/1‑93 (MQ=255)
                                                                             ctctTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCTGCGCCAGATTCAGCACTTTTGAGTCCACCGtctc            <  2:2827447/93‑1 (MQ=255)
                                                                             ctctTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGtctc            <  2:4150326/93‑1 (MQ=255)
                                                                              tctTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTctct           <  1:922876/93‑1 (MQ=255)
                                                                              tctTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTctct           <  1:2697912/93‑1 (MQ=255)
                                                                              tctTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTctct           >  1:1041822/1‑93 (MQ=255)
                                                                                 tGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTAcc        >  2:2418627/1‑93 (MQ=255)
                                                                                  ggTCAGGCCCATCTGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCg       <  1:4257891/93‑1 (MQ=255)
                                                                                      aGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAg   <  1:1659822/93‑1 (MQ=255)
                                                                                       ggCNCNTCNGTAATCAACTCGCTGNCGGANTGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAgc  <  2:2883318/93‑1 (MQ=255)
                                                                                       ggCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAgc  <  2:2959582/93‑1 (MQ=255)
                                                                                          |                                                                                         
GCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAGC  >  NC_000913/1765601‑1765780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ 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
CGCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAGC  >  NC_000913/1765600‑1765780
                                                                                           |                                                                                         
CGCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCA                                                                                         <  SRR4302544.434762/94‑1 (MQ=60)
CGCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCA                                                                                         >  SRR4302544.4247394/1‑94 (MQ=60)
  CACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATC                                                                                       >  SRR4302544.4746970/1‑94 (MQ=60)
  CACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATC                                                                                       >  SRR4302544.1298466/1‑94 (MQ=60)
   cccGAGTGCATTTCCCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCG                                                                                      <  SRR4302544.3654064/91‑1 (MQ=60)
    CAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGG                                                                                     >  SRR4302544.3168913/1‑94 (MQ=60)
        GTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAAT                                                                                 <  SRR4302544.4224980/94‑1 (MQ=60)
           CATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAA                                                                              >  SRR4302544.1052319/1‑94 (MQ=60)
            ATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAAC                                                                             >  SRR4302544.4743277/1‑94 (MQ=60)
            ATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAAC                                                                             >  SRR4302544.2547010/1‑94 (MQ=60)
              TTACCCTCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCATCCAGACCATCTCTTGGTCAGGCGCATCGGTAATCAACTC                                                                           <  SRR4302544.2886436/94‑1 (MQ=60)
              TTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTC                                                                           >  SRR4302544.4194167/1‑94 (MQ=60)
               TACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCG                                                                          <  SRR4302544.2742534/94‑1 (MQ=60)
                 CCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCT                                                                        >  SRR4302544.2090064/1‑94 (MQ=60)
                 CCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCT                                                                        <  SRR4302544.2296574/94‑1 (MQ=60)
                  CCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTG                                                                       <  SRR4302544.359763/94‑1 (MQ=60)
                    GCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGAC                                                                     >  SRR4302544.2318720/1‑94 (MQ=60)
                     CTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACG                                                                    <  SRR4302544.492232/94‑1 (MQ=60)
                     CTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACG                                                                    >  SRR4302544.2113358/1‑94 (MQ=60)
                     CTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACG                                                                    <  SRR4302544.2339528/94‑1 (MQ=60)
                      TCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACTG                                                                   >  SRR4302544.4153418/1‑94 (MQ=60)
                         TCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAAT                                                                <  SRR4302544.3192627/94‑1 (MQ=60)
                          CAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATG                                                               >  SRR4302544.1143019/1‑94 (MQ=60)
                          CAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATG                                                               <  SRR4302544.1567634/94‑1 (MQ=60)
                           AATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGC                                                              >  SRR4302544.1232623/1‑94 (MQ=60)
                           AATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGC                                                              <  SRR4302544.4150568/94‑1 (MQ=60)
                               AGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGA                                                          <  SRR4302544.2867562/94‑1 (MQ=60)
                                   CCTCATCATCACCAGCAAATTCCAAAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAAT                                                      <  SRR4302544.3501413/94‑1 (MQ=60)
                                    CTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATA                                                     >  SRR4302544.1974753/1‑94 (MQ=60)
                                       ATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCT                                                  >  SRR4302544.1279505/1‑94 (MQ=60)
                                        TCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTT                                                 <  SRR4302544.1920629/94‑1 (MQ=60)
                                        TCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTT                                                 <  SRR4302544.3075276/94‑1 (MQ=60)
                                        TCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTT                                                 <  SRR4302544.3075275/94‑1 (MQ=60)
                                         CATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTC                                                <  SRR4302544.4169786/94‑1 (MQ=60)
                                            CTCCAGCAAATTCCTCAATGTTCAGCGCGATCATCTCTTGGTCAGGCGCATCGGTAATCATCTCGCTGACGGAATGCCAGACAATATCTTCCCG                                             <  SRR4302544.2457809/94‑1 (MQ=60)
                                            CACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCG                                             >  SRR4302544.2518664/1‑94 (MQ=60)
                                             ACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGC                                            >  SRR4302544.2144604/1‑94 (MQ=60)
                                              CCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCG                                           >  SRR4302544.3629924/1‑94 (MQ=60)
                                                  CAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAG                                       <  SRR4302544.162520/94‑1 (MQ=60)
                                                  CAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAG                                       <  SRR4302544.3820294/94‑1 (MQ=60)
                                                   AAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGA                                      >  SRR4302544.372964/1‑94 (MQ=60)
                                                     ATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATT                                    <  SRR4302544.1965365/94‑1 (MQ=60)
                                                      TTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTC                                   <  SRR4302544.188008/94‑1 (MQ=60)
                                                          CCAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCA                               <  SRR4302544.563776/94‑1 (MQ=60)
                                                           CAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCAC                              <  SRR4302544.4375016/94‑1 (MQ=60)
                                                           CAATGTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCAC                              >  SRR4302544.124150/1‑94 (MQ=60)
                                                              TGTGCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTT                           <  SRR4302544.2382648/94‑1 (MQ=60)
                                                               GTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTT                          <  SRR4302544.883413/94‑1 (MQ=60)
                                                               GTTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTT                          >  SRR4302544.3286332/1‑94 (MQ=60)
                                                                TTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGTCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTG                         >  SRR4302544.679213/1‑94 (MQ=60)
                                                                TTCAGCCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTGTG                         >  SRR4302544.4699974/1‑94 (MQ=60)
                                                                  CAGCCCGAGCCTCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAG                       <  SRR4302544.1096856/94‑1 (MQ=60)
                                                                     CCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCC                    >  SRR4302544.1754814/1‑94 (MQ=60)
                                                                     CCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCC                    >  SRR4302544.3028135/1‑94 (MQ=60)
                                                                     CCCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCC                    >  SRR4302544.2909871/1‑94 (MQ=60)
                                                                      CCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCA                   >  SRR4302544.1190539/1‑94 (MQ=60)
                                                                      CCGAGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCA                   <  SRR4302544.2691298/94‑1 (MQ=60)
                                                                         AGCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCG                >  SRR4302544.990282/1‑94 (MQ=60)
                                                                          GCATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGT               >  SRR4302544.316523/1‑94 (MQ=60)
                                                                            ATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCT             >  SRR4302544.3487884/1‑94 (MQ=60)
                                                                            ATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCT             >  SRR4302544.1075775/1‑94 (MQ=60)
                                                                            ATCTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCT             >  SRR4302544.667900/1‑94 (MQ=60)
                                                                              CTCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCT           >  SRR4302544.1052159/1‑94 (MQ=60)
                                                                               TCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTA          <  SRR4302544.2723829/94‑1 (MQ=60)
                                                                               TCTTGGTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTA          <  SRR4302544.931974/94‑1 (MQ=60)
                                                                                  TGGTCATGCGCACCGGCAATGAACTCGCCGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCG       <  SRR4302544.2722743/94‑1 (MQ=60)
                                                                                   GGTCAGGCCCATCTGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGA      <  SRR4302544.4301302/94‑1 (MQ=60)
                                                                                    GTCAGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAA     >  SRR4302544.1783467/1‑94 (MQ=60)
                                                                                       AGGCGCATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAGC  <  SRR4302544.1676168/94‑1 (MQ=60)
                                                                                           |                                                                                         
CGCACAGAGTGCATTTACCCGCTCATCAATCAGCGCCTCATCATCACCAGCAAATTCCACAATGTTCAGCCCGAGCATCTCTTGGTCAGGCACATCGGTAATCAACTCGCTGACGGAATGCCAGACAATATCTTCCCGCGCCAGATTCAGCACTTTTGAGTCCACCGTCTCTACCGAAAGC  >  NC_000913/1765600‑1765780

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑