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 1,768,647 T→C A12A (GCT→GCC)  b1689 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,768,6470TC98.3% 374.7 / ‑2.2 119A12A (GCT→GCC) b1689hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (2/0);  new base C (65/52);  total (67/52)
Fisher's exact test for biased strand distribution p-value = 5.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.65e-01

Only 100 of 121 total aligned reads displayed.

GATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCT  >  NC_000913/1768557‑1768735
                                                                                          |                                                                                        
gATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTa                                                                                        <  2:851162/93‑1 (MQ=255)
gATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTa                                                                                        <  2:4117673/93‑1 (MQ=255)
 aTACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTAt                                                                                       <  1:2460562/93‑1 (MQ=255)
  tACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATg                                                                                      >  1:3459470/1‑93 (MQ=255)
      gtgACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACt                                                                                  <  1:4187133/93‑1 (MQ=255)
        gACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTcc                                                                                <  2:2176101/93‑1 (MQ=255)
         gctctctTCAAGCCGTAAGCAGGCTGATAAAGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACTATGAACGCCTATGAACTCCa                                                                               <  2:1889373/92‑1 (MQ=255)
         aCTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCa                                                                               <  2:2560422/93‑1 (MQ=255)
         aCTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCa                                                                               >  1:1599105/1‑93 (MQ=255)
            ctctTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGc                                                                            >  2:1592474/1‑93 (MQ=255)
            ctctTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGc                                                                            >  1:1987078/1‑93 (MQ=255)
               ttCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACt                                                                         <  2:1564118/93‑1 (MQ=255)
                tCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTc                                                                        >  1:4610050/1‑93 (MQ=255)
                  aaGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCg                                                                      >  1:1203409/1‑93 (MQ=255)
                    gCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGcc                                                                    >  2:345004/1‑93 (MQ=255)
                     ccGTCAGCAGGCTGATAATGTTATTTATATTTTATAGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCa                                                                   >  2:312286/1‑93 (MQ=255)
                       gTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCata                                                                 <  2:4636740/93‑1 (MQ=255)
                       gTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCata                                                                 >  2:1648677/1‑93 (MQ=255)
                        tCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCatat                                                                >  1:2174051/1‑93 (MQ=255)
                             agGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTg                                                           >  2:3828628/1‑93 (MQ=255)
                              ggCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGc                                                          >  2:189773/1‑93 (MQ=255)
                                cTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCa                                                        >  1:4303055/1‑93 (MQ=255)
                                 tGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCAt                                                       <  1:2214301/93‑1 (MQ=255)
                                  gttAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATg                                                      >  2:1154724/3‑93 (MQ=255)
                                    tAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGAc                                                    <  2:1874341/93‑1 (MQ=255)
                                      aTGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTa                                                  <  1:1649078/93‑1 (MQ=255)
                                       tGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTAt                                                 <  2:1326086/93‑1 (MQ=255)
                                        gTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTAtt                                                <  1:4263889/93‑1 (MQ=255)
                                        gTTATTTATATTTTATTGTCTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTAtt                                                <  1:4616462/93‑1 (MQ=255)
                                         ttatttatATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtg                                               <  1:4613111/93‑1 (MQ=255)
                                         ttatttatATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtg                                               >  2:4744285/1‑93 (MQ=255)
                                          tatttatATTTTATTGTTTATTTCATGCAGCCATTACGCGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtga                                              <  2:3375022/93‑1 (MQ=255)
                                           atttatATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtgat                                             <  1:1192602/93‑1 (MQ=255)
                                           atttatATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtgat                                             <  1:3496912/93‑1 (MQ=255)
                                             ttatATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATtgatga                                           <  1:1811586/93‑1 (MQ=255)
                                               atatTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAAt                                         >  1:3746975/1‑93 (MQ=255)
                                               atatTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAAt                                         <  2:1128163/93‑1 (MQ=255)
                                               atatTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAAt                                         <  2:2961015/93‑1 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGACCTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgc                                       <  2:2562602/93‑1 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCCCTCCGCCATATTTTTGCCATGACTATTGATGAATgc                                       <  2:1146062/93‑1 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCTTTACTATTGATGAATgc                                       >  2:2301477/1‑93 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGCCTATTGATGAATgc                                       <  2:2500723/93‑1 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgc                                       >  1:2584902/1‑93 (MQ=255)
                                                 atTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgc                                       <  2:3403421/93‑1 (MQ=255)
                                                  ttttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgcg                                      >  1:2804362/1‑93 (MQ=255)
                                                  ttttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgcg                                      >  2:2529349/1‑93 (MQ=255)
                                                  ttttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgcg                                      >  2:2462332/1‑93 (MQ=255)
                                                   tttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTAAGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATgcgc                                     <  2:3760506/93‑1 (MQ=255)
                                                    ttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGcgcg                                    >  1:3238127/1‑93 (MQ=255)
                                                    ttATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGcgcg                                    <  2:4574130/93‑1 (MQ=255)
                                                      aTTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCTATGACTATTGATGAATGCGCGAc                                  >  1:3708197/1‑93 (MQ=255)
                                                       ttGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGAcc                                 >  2:489114/1‑93 (MQ=255)
                                                       ttGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGAcc                                 <  1:3885169/93‑1 (MQ=255)
                                                       ttGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGAcc                                 <  2:633638/93‑1 (MQ=255)
                                                        tGTTTATTTCATGCAGCCATTACACGGTGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCt                                >  2:613033/1‑93 (MQ=255)
                                                        tGTTTATTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATCTTTTTGCCATGACTATTGATGAATGGGCGACCt                                >  2:4039666/1‑93 (MQ=255)
                                                        tGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCt                                >  2:2804549/1‑93 (MQ=255)
                                                            tATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGAt                            <  2:3843953/93‑1 (MQ=255)
                                                            tATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGAt                            <  1:2870655/93‑1 (MQ=255)
                                                            tATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGAt                            <  1:615239/93‑1 (MQ=255)
                                                             aTTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGAtt                           >  2:4026034/1‑93 (MQ=255)
                                                             aTTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGAtt                           >  2:3815528/1‑93 (MQ=255)
                                                             aTTTCATGCAGCCATTACACGACGAATGCCTATGAACTCCAGTCACTCCGCCATATTTTTGCCATGACTATTGGTGAATGCGCGACCTGGAtg                           >  1:322817/1‑92 (MQ=255)
                                                              tttCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTg                          >  2:3412683/1‑93 (MQ=255)
                                                                tCAGGCAGCCATTACACGATGAGCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGcc                        <  1:1912297/93‑1 (MQ=255)
                                                                 caagCAGCCATTGCACGATGAACGCCTACGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGccc                       <  2:712809/90‑1 (MQ=255)
                                                                 cATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGccc                       >  1:2652294/1‑93 (MQ=255)
                                                                  aTGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCa                      <  1:4692130/93‑1 (MQ=255)
                                                                    gCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGa                    >  1:22293/1‑93 (MQ=255)
                                                                    gCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGa                    >  1:4512827/1‑93 (MQ=255)
                                                                    gCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGa                    <  2:3880821/93‑1 (MQ=255)
                                                                     cAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGAc                   <  2:152146/93‑1 (MQ=255)
                                                                      aGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGAcc                  >  2:587247/1‑93 (MQ=255)
                                                                      aGCCATTACACGATGAACGCCTATGAACTCCACGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCCGAcc                  >  1:4311259/1‑93 (MQ=255)
                                                                       gCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCg                 >  1:549140/1‑93 (MQ=255)
                                                                       gCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCg                 >  1:3276465/1‑93 (MQ=255)
                                                                       gCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCg                 >  1:558467/1‑93 (MQ=255)
                                                                       gCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCg                 >  1:3276464/1‑93 (MQ=255)
                                                                       gCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCg                 >  2:158884/1‑93 (MQ=255)
                                                                        ccATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCgg                >  2:4000364/1‑93 (MQ=255)
                                                                        ccATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCgg                <  1:2580477/93‑1 (MQ=255)
                                                                         cATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGTTTGCCCAGCCCGGt               >  1:1468608/1‑93 (MQ=255)
                                                                         cATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGt               >  1:1468459/1‑93 (MQ=255)
                                                                         cATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGt               <  2:4059283/93‑1 (MQ=255)
                                                                          aTTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTg              >  2:2379699/1‑93 (MQ=255)
                                                                          aTTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCACAGACCGGTg              >  2:2379696/1‑93 (MQ=255)
                                                                           ttACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGa             >  1:3218303/1‑93 (MQ=255)
                                                                           ttACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGa             >  1:863826/1‑93 (MQ=255)
                                                                            tACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGAc            >  2:2646257/1‑93 (MQ=255)
                                                                             acacGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACa           >  1:2696780/1‑93 (MQ=255)
                                                                              cacGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAg          >  2:259642/1‑93 (MQ=255)
                                                                              cacGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAg          >  2:1093641/1‑93 (MQ=255)
                                                                               acGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGt         >  1:1608193/1‑93 (MQ=255)
                                                                                 gATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGa       >  1:4177232/1‑93 (MQ=255)
                                                                                    gAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAg    >  2:2289616/1‑93 (MQ=255)
                                                                                    gAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAg    <  1:1285191/93‑1 (MQ=255)
                                                                                      aCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACGTGGATTGCCCAGACCGGTGACAGTGAAAGCt  <  1:231175/93‑1 (MQ=255)
                                                                                      aCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCt  >  1:2497102/1‑93 (MQ=255)
                                                                                      aCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCt  <  2:1730975/93‑1 (MQ=255)
                                                                                      aCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCt  >  1:1958252/1‑93 (MQ=255)
                                                                                          |                                                                                        
GATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCT  >  NC_000913/1768557‑1768735

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ 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
CAAGATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCTGGCGT  >  NC_000913/1768554‑1768740
                                                                                             |                                                                                             
CAAGATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCC                                                                                               >  SRR4302544.3676674/1‑94 (MQ=60)
    ATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATG                                                                                           >  SRR4302544.3492492/1‑94 (MQ=60)
    ATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATG                                                                                           <  SRR4302544.2484050/94‑1 (MQ=60)
         GTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTC                                                                                      <  SRR4302544.4228601/94‑1 (MQ=60)
           GACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCA                                                                                    >  SRR4302544.1614870/1‑94 (MQ=60)
             CTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGG                                                                                  <  SRR4302544.4726745/94‑1 (MQ=60)
              TCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGC                                                                                 >  SRR4302544.2006371/1‑94 (MQ=60)
                  TTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTC                                                                             >  SRR4302544.4655835/1‑94 (MQ=60)
                    CAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCG                                                                           >  SRR4302544.1215332/1‑94 (MQ=60)
                          GTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATAT                                                                     >  SRR4302544.2194652/1‑94 (MQ=60)
                                  GCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCA                                                             >  SRR4302544.4346947/1‑94 (MQ=60)
                                    TGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATG                                                           >  SRR4302544.3424499/1‑94 (MQ=60)
                                    TGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATG                                                           <  SRR4302544.2235133/94‑1 (MQ=60)
                                         ATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTAT                                                      <  SRR4302544.1665349/94‑1 (MQ=60)
                                           GTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTG                                                    <  SRR4302544.4307385/94‑1 (MQ=60)
                                           GTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTG                                                    <  SRR4302544.2305488/94‑1 (MQ=60)
                                           GTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTG                                                    <  SRR4302544.4498991/94‑1 (MQ=60)
                                           GTTATTTATATTTTATTGTCTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTG                                                    <  SRR4302544.4662289/94‑1 (MQ=60)
                                            TTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGA                                                   <  SRR4302544.4658917/94‑1 (MQ=60)
                                              ATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATG                                                 <  SRR4302544.3530258/94‑1 (MQ=60)
                                              ATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATG                                                 <  SRR4302544.1204432/94‑1 (MQ=60)
                                                TTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAA                                               <  SRR4302544.1829277/94‑1 (MQ=60)
                                                TTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAA                                               >  SRR4302544.4197085/1‑94 (MQ=60)
                                                 TATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAAT                                              >  SRR4302544.3784198/1‑94 (MQ=60)
                                                  ATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATG                                             <  SRR4302544.2625740/94‑1 (MQ=60)
                                                  ATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATG                                             <  SRR4302544.3235592/94‑1 (MQ=60)
                                                   TATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGC                                            >  SRR4302544.2609759/1‑94 (MQ=60)
                                                    ATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCG                                           >  SRR4302544.2831400/1‑94 (MQ=60)
                                                      TTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCG                                         >  SRR4302544.3269116/1‑94 (MQ=60)
                                                      TTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCG                                         >  SRR4302544.1608973/1‑94 (MQ=60)
                                                        TATTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCTATGACTATTGATGAATGCGCGAC                                       >  SRR4302544.3745088/1‑94 (MQ=60)
                                                          TTGTTTATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCT                                     <  SRR4302544.3923756/94‑1 (MQ=60)
                                                               TATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATT                                <  SRR4302544.2898362/94‑1 (MQ=60)
                                                               TATTTCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATT                                <  SRR4302544.621277/94‑1 (MQ=60)
                                                               TATTTCATGCAGCCATTACACGACGAATGCCTATGAACTCCAGTCACTCCGCCATATTTTTGCCATGACTATTGGTGAATGCGCGACCTGGATG                                >  SRR4302544.326171/1‑94 (MQ=60)
                                                                   TCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCC                            >  SRR4302544.2677727/1‑94 (MQ=60)
                                                                   TCATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCC                            <  SRR4302544.1930780/94‑1 (MQ=60)
                                                                   TCAGGCAGCCATTACACGATGAGCGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCC                            <  SRR4302544.1930779/94‑1 (MQ=60)
                                                                     ATGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAG                          <  SRR4302544.4738476/94‑1 (MQ=60)
                                                                      TGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGA                         >  SRR4302544.22509/1‑94 (MQ=60)
                                                                      TGCAGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGA                         >  SRR4302544.4558044/1‑94 (MQ=60)
                                                                        CAGCCATTACACGATGAACGCCTATGAACTCCACGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCCGACC                       >  SRR4302544.4355197/1‑94 (MQ=60)
                                                                         AGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCG                      >  SRR4302544.3307693/1‑94 (MQ=60)
                                                                         AGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCG                      >  SRR4302544.3307694/1‑94 (MQ=60)
                                                                         AGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCG                      >  SRR4302544.563929/1‑94 (MQ=60)
                                                                         AGCCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCG                      >  SRR4302544.554523/1‑94 (MQ=60)
                                                                           CCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGTTTGCCCAGCCCGGT                    >  SRR4302544.1483164/1‑94 (MQ=60)
                                                                           CCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGT                    <  SRR4302544.2605274/94‑1 (MQ=60)
                                                                           CCATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGT                    >  SRR4302544.1483015/1‑94 (MQ=60)
                                                                             ATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGA                  >  SRR4302544.872371/1‑94 (MQ=60)
                                                                             ATTACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGA                  >  SRR4302544.3249007/1‑94 (MQ=60)
                                                                               TACACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACA                >  SRR4302544.2722679/1‑94 (MQ=60)
                                                                                 CACGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGT              >  SRR4302544.1624047/1‑94 (MQ=60)
                                                                                   CGATGAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGA            >  SRR4302544.4218609/1‑94 (MQ=60)
                                                                                       GAACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGC        <  SRR4302544.1297851/94‑1 (MQ=60)
                                                                                        AACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCT       >  SRR4302544.1977249/1‑94 (MQ=60)
                                                                                        AACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCT       >  SRR4302544.2521032/1‑94 (MQ=60)
                                                                                         ACGCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACGTGGATTGCCCAGACCGGTGACAGTGAAAGCTG      <  SRR4302544.233586/94‑1 (MQ=60)
                                                                                           GCCTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCTGGC    >  SRR4302544.367578/1‑94 (MQ=60)
                                                                                             CTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCTGGCGC  >  SRR4302544.4183435/1‑94 (MQ=60)
                                                                                             |                                                                                             
CAAGATACTGTGACTCTCTTCAAGCCGTCAGCAGGCTGATAATGTTATTTATATTTTATTGTTTATTTCATGCAGCCATTACACGATGAACGCTTATGAACTCCAGGCACTCCGCCATATTTTTGCCATGACTATTGATGAATGCGCGACCTGGATTGCCCAGACCGGTGACAGTGAAAGCTGGCGT  >  NC_000913/1768554‑1768740

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑