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 1,845,852 T→C T61A (ACC→GCC)  selD ← selenophosphate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,845,8520TC97.7% 395.9 / ‑1.0 129T61A (ACC→GCC) selDselenophosphate synthase
Reads supporting (aligned to +/- strand):  ref base T (2/1);  new base C (74/52);  total (76/53)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 133 total aligned reads displayed.

CGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTAT  >  NC_000913/1845762‑1845941
                                                                                          |                                                                                         
cGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGgcgc                                                                                         >  2:4521593/1‑93 (MQ=255)
 gCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGcc                                                                                        >  1:4259820/1‑93 (MQ=255)
  cTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATGAAGAAGTCGGTGGTACTGATAACGCTGGCGCCa                                                                                       <  1:4066404/93‑1 (MQ=255)
   tGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCAt                                                                                      >  2:1625241/1‑93 (MQ=255)
   tGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCAt                                                                                      >  2:1004525/1‑93 (MQ=255)
        gCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGccc                                                                                 <  1:3376527/93‑1 (MQ=255)
          gTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAg                                                                               >  1:2904218/1‑93 (MQ=255)
           ttAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGa                                                                              >  2:681491/1‑93 (MQ=255)
           ttAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGa                                                                              <  1:3868407/93‑1 (MQ=255)
           ttAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGa                                                                              <  1:378849/93‑1 (MQ=255)
           ttAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGa                                                                              >  2:2842611/1‑93 (MQ=255)
            tAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGAt                                                                             <  2:1083623/93‑1 (MQ=255)
             aGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATc                                                                            >  1:4030993/1‑93 (MQ=255)
                cgccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGTTACTGATAACGCTGGCGCCATTGCCCAGATCGTa                                                                         <  2:2974216/93‑1 (MQ=255)
                cgccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTa                                                                         <  1:1119776/93‑1 (MQ=255)
                cgccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGACGCCATTGCCCAGATCGTa                                                                         <  2:1966589/93‑1 (MQ=255)
                 gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                        >  1:1402387/1‑93 (MQ=255)
                 gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                        >  2:4581272/1‑93 (MQ=255)
                   cgcAATGCGGCCAAAATCGAAAGGACTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTacac                                                                      <  1:3445359/93‑1 (MQ=255)
                    gcAATGGGGCCAAAATCGAAAGGAATATGAACGATTGGCATAAAGAGGTGGGTGGTAGTAATAACGCGGGCGCCATAGTTCAGATCGTacacg                                                                     >  2:3977645/1‑92 (MQ=255)
                    gcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAcc                                                                     >  1:3745414/1‑93 (MQ=255)
                        tGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAccgccg                                                                 >  2:286422/1‑93 (MQ=255)
                        tGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAccgccg                                                                 >  2:1933933/1‑93 (MQ=255)
                          cGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCa                                                               >  2:3543066/1‑93 (MQ=255)
                           ggCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAt                                                              <  1:701066/93‑1 (MQ=255)
                            gCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtc                                                             <  1:3398428/93‑1 (MQ=255)
                            gCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtc                                                             <  1:678916/93‑1 (MQ=255)
                            gCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtc                                                             <  2:1267390/93‑1 (MQ=255)
                              cAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgt                                                           >  2:659884/1‑93 (MQ=255)
                              cAAAATCGAAAGGATCATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgt                                                           <  2:4396982/93‑1 (MQ=255)
                               aaaaTCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgtc                                                          >  1:897642/1‑93 (MQ=255)
                               aaaaTCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgtc                                                          >  1:4426147/1‑93 (MQ=255)
                                 aaTCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTcgc                                                        <  2:3098603/93‑1 (MQ=255)
                                   acGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCgg                                                      <  1:3521087/92‑1 (MQ=255)
                                   acGAAAGGATTATCAACGATCGGCAGAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCgg                                                      <  1:2745592/92‑1 (MQ=255)
                                    cGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCggg                                                     <  1:2494017/93‑1 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    >  1:816353/1‑93 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    >  1:816354/1‑93 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    >  1:2182472/1‑93 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    >  2:1340356/1‑93 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    <  2:689367/93‑1 (MQ=255)
                                     gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                    <  1:2820687/93‑1 (MQ=255)
                                      aaaGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGtt                                                   >  2:1063892/1‑93 (MQ=255)
                                      aaaGGATTATCAACGATCGGCATAAAGAAGTCGGGGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGtt                                                   >  1:1801133/1‑93 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 >  2:1900582/1‑93 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 >  2:4399152/1‑93 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 <  2:3363301/93‑1 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 >  1:916093/1‑93 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 <  1:3102752/93‑1 (MQ=255)
                                        aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                 >  2:2292556/1‑93 (MQ=255)
                                         ggATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCa                                                <  2:1943759/93‑1 (MQ=255)
                                         ggATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCa                                                <  2:1727116/93‑1 (MQ=255)
                                         ggATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCa                                                >  1:2180912/1‑93 (MQ=255)
                                          gATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAt                                               >  2:3543123/1‑93 (MQ=255)
                                          gATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAt                                               >  1:4391102/1‑93 (MQ=255)
                                          gATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAt                                               >  1:1337062/1‑93 (MQ=255)
                                           aTTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAtt                                              <  1:3655915/93‑1 (MQ=255)
                                           aTTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAtt                                              >  2:3086698/1‑93 (MQ=255)
                                           aTTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAtt                                              >  2:559391/1‑93 (MQ=255)
                                           aTTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGATTCAtt                                              >  1:4535359/1‑93 (MQ=255)
                                             tATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAc                                            <  2:1994726/93‑1 (MQ=255)
                                              aTCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAcc                                           >  1:3337381/1‑93 (MQ=255)
                                               tCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAccc                                          >  2:3754383/1‑93 (MQ=255)
                                                cAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCca                                         >  2:4690198/1‑93 (MQ=255)
                                                 aaCGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCcac                                        >  2:3624548/1‑93 (MQ=255)
                                                   cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                      <  1:1002409/93‑1 (MQ=255)
                                                   cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                      <  1:1952915/93‑1 (MQ=255)
                                                    gATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAg                                     >  2:2067332/1‑93 (MQ=255)
                                                         gCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAt                                >  2:1690737/1‑93 (MQ=255)
                                                           aTAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTc                              >  1:487006/1‑93 (MQ=255)
                                                            tAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCg                             >  2:4540403/1‑93 (MQ=255)
                                                            tAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCg                             >  2:4540402/1‑93 (MQ=255)
                                                            tAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCg                             >  1:1011375/1‑93 (MQ=255)
                                                             aaaGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCgg                            <  2:3909710/93‑1 (MQ=255)
                                                              aagaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGa                           >  1:4254010/1‑93 (MQ=255)
                                                               agaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAt                          <  1:1164629/93‑1 (MQ=255)
                                                               agaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAt                          >  2:1342812/1‑93 (MQ=255)
                                                               agaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAt                          <  1:2487565/93‑1 (MQ=255)
                                                                gaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATc                         <  1:3186831/93‑1 (MQ=255)
                                                                gaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATc                         >  2:4276031/1‑93 (MQ=255)
                                                                  agTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaa                       >  1:796728/1‑93 (MQ=255)
                                                                    tCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaaca                     >  2:766462/1‑93 (MQ=255)
                                                                      ggtggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACaaa                   <  2:2270033/93‑1 (MQ=255)
                                                                        tggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACt                 >  2:3650096/1‑93 (MQ=255)
                                                                         ggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACtt                >  2:2445143/1‑93 (MQ=255)
                                                                          gtACTGATAACGCTGGCGCCCTTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTc               <  2:3400131/93‑1 (MQ=255)
                                                                            aCTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGc             >  1:3536123/1‑93 (MQ=255)
                                                                             cTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGcc            <  1:1412041/93‑1 (MQ=255)
                                                                             cTGATAACCCCGGCGCCCATGCCCAGATCGTACCCCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGcc            <  1:982441/93‑1 (MQ=255)
                                                                              tGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCt           <  2:2408272/93‑1 (MQ=255)
                                                                              tGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCt           <  2:4450766/93‑1 (MQ=255)
                                                                              tGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCt           <  2:2238586/93‑1 (MQ=255)
                                                                               gATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTg          >  1:246184/1‑93 (MQ=255)
                                                                                 tAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCt        >  1:3629034/1‑93 (MQ=255)
                                                                                 tAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCt        >  2:4483096/1‑93 (MQ=255)
                                                                                 tAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCt        >  1:2015975/1‑93 (MQ=255)
                                                                                  aaCGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTc       >  1:4409487/1‑93 (MQ=255)
                                                                                     gCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACt    <  2:2225349/93‑1 (MQ=255)
                                                                                      cTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTa   >  1:2186854/1‑93 (MQ=255)
                                                                                      cTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTa   >  2:439680/1‑93 (MQ=255)
                                                                                          |                                                                                         
CGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTAT  >  NC_000913/1845762‑1845941

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

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGC  >  NC_000913/1845759‑1845943
                                                                                             |                                                                                           
TATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGC                                                                                             <  SRR4302544.4129588/94‑1 (MQ=60)
 ATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCG                                                                                            >  SRR4302544.3975137/1‑94 (MQ=60)
   CGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCC                                                                                          >  SRR4302544.4303257/1‑94 (MQ=60)
     CTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATGAAGAAGTCGGTGGTACTGATAACGCTGGCGCCAT                                                                                        <  SRR4302544.4106891/94‑1 (MQ=60)
           GCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCA                                                                                  <  SRR4302544.3408757/94‑1 (MQ=60)
            CGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAG                                                                                 >  SRR4302544.2932181/1‑94 (MQ=60)
             GTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGA                                                                                >  SRR4302544.848657/1‑94 (MQ=60)
              TTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGAT                                                                               <  SRR4302544.3906817/94‑1 (MQ=60)
              TTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGAT                                                                               <  SRR4302544.382709/94‑1 (MQ=60)
               TAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATC                                                                              >  SRR4302544.4071146/1‑94 (MQ=60)
               TAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATC                                                                              >  SRR4302544.3481464/1‑94 (MQ=60)
                   ctcctCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTAC                                                                          <  SRR4302544.2686689/89‑1 (MQ=60)
                   CGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTAC                                                                          >  SRR4302544.1416357/1‑94 (MQ=60)
                   CGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTAC                                                                          <  SRR4302544.1130946/94‑1 (MQ=60)
                      CGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACC                                                                       >  SRR4302544.3782624/1‑94 (MQ=60)
                      CGCAATGCGGCCAAAATCGAAAGGACTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACC                                                                       <  SRR4302544.3478277/94‑1 (MQ=60)
                          ATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCG                                                                   <  SRR4302544.2619024/94‑1 (MQ=60)
                              GGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATC                                                               <  SRR4302544.708047/94‑1 (MQ=60)
                               GCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCG                                                              <  SRR4302544.3430923/94‑1 (MQ=60)
                               GCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCG                                                              <  SRR4302544.4186076/94‑1 (MQ=60)
                               GCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCG                                                              <  SRR4302544.685646/94‑1 (MQ=60)
                                CCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGT                                                             >  SRR4302544.4438561/1‑94 (MQ=60)
                                 CAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTC                                                            >  SRR4302544.3097347/1‑94 (MQ=60)
                                 CAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTC                                                            >  SRR4302544.4470802/1‑94 (MQ=60)
                                 CAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTC                                                            >  SRR4302544.906521/1‑94 (MQ=60)
                                      TCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGG                                                       <  SRR4302544.4627676/94‑1 (MQ=60)
                                      ACGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGG                                                       <  SRR4302544.3554718/94‑1 (MQ=60)
                                      ACGAAAGGATTATCAACGATCGGCAGAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGG                                                       <  SRR4302544.2772044/94‑1 (MQ=60)
                                       CGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGT                                                      <  SRR4302544.2517913/94‑1 (MQ=60)
                                       CGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGT                                                      >  SRR4302544.2203129/1‑94 (MQ=60)
                                       CGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGT                                                      >  SRR4302544.824326/1‑94 (MQ=60)
                                       CGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGT                                                      >  SRR4302544.824327/1‑94 (MQ=60)
                                        GAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTT                                                     <  SRR4302544.2847933/94‑1 (MQ=60)
                                        GAAAGGATTATCAACGATCGGCATAAAGAAGTCGGGGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTT                                                     >  SRR4302544.1818734/1‑94 (MQ=60)
                                          AAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTC                                                   <  SRR4302544.714646/94‑1 (MQ=60)
                                          AAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTC                                                   >  SRR4302544.925143/1‑94 (MQ=60)
                                           AGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCA                                                  <  SRR4302544.3132282/94‑1 (MQ=60)
                                           AGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCA                                                  >  SRR4302544.2201558/1‑94 (MQ=60)
                                            GGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAT                                                 >  SRR4302544.4435531/1‑94 (MQ=60)
                                            GGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAT                                                 >  SRR4302544.1350251/1‑94 (MQ=60)
                                             GATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGATTCATT                                                >  SRR4302544.4580711/1‑94 (MQ=60)
                                              ATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTA                                               <  SRR4302544.3692392/94‑1 (MQ=60)
                                                TATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACC                                             >  SRR4302544.3369180/1‑94 (MQ=60)
                                                TATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACC                                             >  SRR4302544.3369179/1‑94 (MQ=60)
                                                      CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                       <  SRR4302544.1971854/94‑1 (MQ=60)
                                                      CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                       <  SRR4302544.1012360/94‑1 (MQ=60)
                                                             CATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTC                                >  SRR4302544.491779/1‑94 (MQ=60)
                                                              ATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCG                               >  SRR4302544.1021451/1‑94 (MQ=60)
                                                              ATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCG                               >  SRR4302544.2158388/1‑94 (MQ=60)
                                                               TAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCACTGCCCAGACCGCACACCGCCGCATCGTCGCGGGTGGCATTACCCACAAGCAAATTTGG                              >  SRR4302544.3654652/1‑94 (MQ=60)
                                                                AAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGA                             >  SRR4302544.4297382/1‑94 (MQ=60)
                                                                 AAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAT                            <  SRR4302544.1200552/94‑1 (MQ=60)
                                                                  AGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATC                           <  SRR4302544.1176235/94‑1 (MQ=60)
                                                                  AGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATC                           <  SRR4302544.2511393/94‑1 (MQ=60)
                                                                   GAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCA                          <  SRR4302544.3863640/94‑1 (MQ=60)
                                                                   GAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCA                          <  SRR4302544.3217179/94‑1 (MQ=60)
                                                                    AAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAA                         >  SRR4302544.804455/1‑94 (MQ=60)
                                                                              TACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGC               >  SRR4302544.3569950/1‑94 (MQ=60)
                                                                                CTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCT             <  SRR4302544.1426102/94‑1 (MQ=60)
                                                                                CTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACCTCGCCT             <  SRR4302544.992072/94‑1 (MQ=60)
                                                                                 TGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTG            >  SRR4302544.3692311/1‑94 (MQ=60)
                                                                                 TGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTG            >  SRR4302544.248762/1‑94 (MQ=60)
                                                                                  GATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGC           >  SRR4302544.1438748/1‑94 (MQ=60)
                                                                                   ATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCT          >  SRR4302544.2035555/1‑94 (MQ=60)
                                                                                   ATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCT          >  SRR4302544.3665194/1‑94 (MQ=60)
                                                                                    TAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTC         >  SRR4302544.4454013/1‑94 (MQ=60)
                                                                                        GCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTA     >  SRR4302544.2207528/1‑94 (MQ=60)
                                                                                          TGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATG   <  SRR4302544.2243832/94‑1 (MQ=60)
                                                                                           GGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGC  >  SRR4302544.2053270/1‑94 (MQ=60)
                                                                                             |                                                                                           
TATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGC  >  NC_000913/1845759‑1845943

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑