Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F1 I2 R1	1873	183.1	9376148	98.2%	9207377	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_000913	1,845,852	0	T	C	100.0%	410.9 / NA	132	T61A (ACC→GCC)	selD	selenophosphate synthase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (69/63); total (69/63)

Only 100 of 137 total aligned reads displayed.

CTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTA  >  NC_000913/1845764‑1845940

cTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATAGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCa                                                                                      >  1:973306/1‑93 (MQ=255)

 tGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCAt                                                                                     <  2:195653/93‑1 (MQ=255)

   aTGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTg                                                                                   >  1:1820845/1‑93 (MQ=255)

    tGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGc                                                                                  <  2:1235581/93‑1 (MQ=255)

        gTTATTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAg                                                                              <  2:4066945/93‑1 (MQ=255)

        gTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAg                                                                              >  1:2851707/1‑93 (MQ=255)

         ttAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGa                                                                             <  2:1824270/93‑1 (MQ=255)

           aGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATc                                                                           >  1:2874388/1‑93 (MQ=255)

            gTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCg                                                                          >  1:421473/1‑93 (MQ=255)

            gTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCg                                                                          >  1:3861898/1‑93 (MQ=255)

             tCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGt                                                                         >  1:2717397/1‑93 (MQ=255)

              cgccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTa                                                                        >  1:1474532/1‑93 (MQ=255)

              cgccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTa                                                                        <  2:239984/93‑1 (MQ=255)

               gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                       <  2:2577089/93‑1 (MQ=255)

               gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                       >  1:2432266/1‑93 (MQ=255)

               gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                       <  2:464751/93‑1 (MQ=255)

               gccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTac                                                                       <  1:493984/93‑1 (MQ=255)

                ccgcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGACATTGCCCAGATCGTaca                                                                      >  2:4207208/1‑93 (MQ=255)

                  gcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAcc                                                                    >  1:3254838/1‑93 (MQ=255)

                  gcAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAcc                                                                    >  1:2946416/1‑93 (MQ=255)

                    aaTGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAccgc                                                                  <  1:3092391/93‑1 (MQ=255)

                    aaTGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAccgc                                                                  <  2:1784367/93‑1 (MQ=255)

                     aTGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACAccgcc                                                                 >  1:2234912/1‑93 (MQ=255)

                          gCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtc                                                            <  2:1142985/93‑1 (MQ=255)

                          gCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtc                                                            <  2:2742140/93‑1 (MQ=255)

                           ccAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcg                                                           >  1:4235919/1‑93 (MQ=255)

                            cAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgt                                                          >  1:624313/1‑93 (MQ=255)

                            cAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgt                                                          <  1:1649753/93‑1 (MQ=255)

                            cAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGCGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgt                                                          >  1:1026934/1‑93 (MQ=255)

                              aaaTCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCAtcgtcg                                                        >  2:1447545/1‑93 (MQ=255)

                                 tCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCgg                                                     <  2:431996/93‑1 (MQ=255)

                                   gAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGt                                                   <  2:833484/93‑1 (MQ=255)

                                     aaGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGttt                                                 >  2:589469/1‑93 (MQ=255)

                                     aaGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGttt                                                 >  2:1939398/1‑93 (MQ=255)

                                     aaGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGttt                                                 <  2:2200306/93‑1 (MQ=255)

                                     aaGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGttt                                                 >  1:1199127/1‑93 (MQ=255)

                                      aGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTc                                                >  2:4254397/1‑93 (MQ=255)

                                       ggATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCa                                               >  1:1470763/1‑93 (MQ=255)

                                       ggATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCa                                               <  2:3240392/93‑1 (MQ=255)

                                        gATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAt                                              <  1:4408884/93‑1 (MQ=255)

                                          ttATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACGCCGCCGCATCGTCGCGGGTTTCATTa                                            >  2:3794457/1‑93 (MQ=255)

                                           tATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAc                                           >  1:4278817/1‑93 (MQ=255)

                                           tATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAc                                           <  1:2639467/93‑1 (MQ=255)

                                           tATCAACAATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAc                                           <  2:3123113/93‑1 (MQ=255)

                                            aTCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAcc                                          <  2:692198/93‑1 (MQ=255)

                                             tCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAccc                                         >  2:1994209/1‑93 (MQ=255)

                                             tCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAccc                                         >  2:1062362/1‑93 (MQ=255)

                                              cAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCca                                        <  2:1870126/93‑1 (MQ=255)

                                               aaCGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCcac                                       >  1:1858980/1‑93 (MQ=255)

                                                aCGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCcaca                                      >  2:1131027/1‑93 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     >  2:2872198/1‑93 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     <  1:2890584/93‑1 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     <  2:1537946/93‑1 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     <  1:214117/93‑1 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     <  1:362203/93‑1 (MQ=255)

                                                 cGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACaa                                     <  1:3726957/93‑1 (MQ=255)

                                                   aTCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGc                                   >  1:2800172/1‑93 (MQ=255)

                                                    tCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCa                                  >  2:2672748/1‑93 (MQ=255)

                                                     cGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCaa                                 <  2:398169/93‑1 (MQ=255)

                                                      ggCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCaaa                                <  2:1891391/93‑1 (MQ=255)

                                                      ggCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCaaa                                <  2:3992050/93‑1 (MQ=255)

                                                       gCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAt                               >  1:1262343/1‑93 (MQ=255)

                                                       gCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAt                               >  2:508768/1‑93 (MQ=255)

                                                        cATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAtt                              <  1:629099/93‑1 (MQ=255)

                                                        cATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAtt                              >  1:4486376/1‑93 (MQ=255)

                                                        cATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACACACAAGCAAAtt                              >  2:2284117/1‑93 (MQ=255)

                                                         aTAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCTCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTc                             >  2:2851151/1‑93 (MQ=255)

                                                          tAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCg                            >  2:1090154/1‑93 (MQ=255)

                                                            aagaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGa                          <  2:1736723/93‑1 (MQ=255)

                                                            aagaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGa                          >  2:3592415/1‑93 (MQ=255)

                                                            aagaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGa                          >  2:3464448/1‑93 (MQ=255)

                                                             agaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAt                         >  1:953495/1‑93 (MQ=255)

                                                             agaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAt                         >  1:2217088/1‑93 (MQ=255)

                                                              gaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAGATTCGGAta                        >  1:4386710/1‑92 (MQ=255)

                                                              gaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATc                        <  1:373983/93‑1 (MQ=255)

                                                              aaagTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCAATCCCCACAAGCAAATTCGGATc                        <  2:3225948/92‑1 (MQ=255)

                                                                agTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaa                      >  1:109852/1‑93 (MQ=255)

                                                                  tCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaaca                    <  2:2332801/93‑1 (MQ=255)

                                                                  tCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaaca                    >  2:79885/1‑93 (MQ=255)

                                                                   cGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATcaacaa                   <  1:3063919/93‑1 (MQ=255)

                                                                    ggtggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACaaa                  >  1:1167575/1‑93 (MQ=255)

                                                                       ggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACtt               >  2:1523203/1‑93 (MQ=255)

                                                                       ggtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACtt               <  2:4605395/93‑1 (MQ=255)

                                                                        gtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTc              <  1:3419668/93‑1 (MQ=255)

                                                                        gtACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTc              <  1:2459355/93‑1 (MQ=255)

                                                                        gtACTGAGAACGCTGGCGCCATTGCCCAGATCATACACCGCCCCATCGTCGCAGGTTTCATTCCCCACAAGCAAATTCGGACCAACAAACTTc              <  1:221936/93‑1 (MQ=255)

                                                                           cTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGcc           <  1:3461025/93‑1 (MQ=255)

                                                                            tGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCt          <  1:707065/93‑1 (MQ=255)

                                                                             gATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTg         >  2:3197507/1‑93 (MQ=255)

                                                                              aTAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGc        <  2:2321034/93‑1 (MQ=255)

                                                                              aTAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGc        <  1:1553897/93‑1 (MQ=255)

                                                                              aTAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGc        <  2:3518067/93‑1 (MQ=255)

                                                                               aaaCGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCt       <  1:1731339/92‑1 (MQ=255)

                                                                                 aCGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCa     >  1:2734458/1‑93 (MQ=255)

                                                                                  cGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCAc    <  1:4540267/93‑1 (MQ=255)

                                                                                  cGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCAc    >  2:366989/1‑93 (MQ=255)

                                                                                  cGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCAc    <  1:3755390/93‑1 (MQ=255)

                                                                                    cTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTa  <  1:1004048/93‑1 (MQ=255)

                                                                                    cTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTa  <  2:1559368/93‑1 (MQ=255)

                                                                                    cTGGCGCCATTGCACAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTa  <  1:2677390/93‑1 (MQ=255)

CTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTA  >  NC_000913/1845764‑1845940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `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

ATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGCAG  >  NC_000913/1845760‑1845945

ATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCG                                                                                              >  SRR4302535.4305492/1‑94 (MQ=60)

   GCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATAGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCA                                                                                           >  SRR4302535.980213/1‑94 (MQ=60)

     TGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATT                                                                                         <  SRR4302535.2361445/94‑1 (MQ=60)

      GATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTG                                                                                        >  SRR4302535.1834001/1‑94 (MQ=60)

        TGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCC                                                                                      <  SRR4302535.3578148/94‑1 (MQ=60)

          GCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCA                                                                                    <  SRR4302535.4542325/94‑1 (MQ=60)

           CGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAG                                                                                   >  SRR4302535.2871914/1‑94 (MQ=60)

              TAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATC                                                                                >  SRR4302535.2894756/1‑94 (MQ=60)

              TAGTCGCCGCAATGCGGACAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATC                                                                                <  SRR4302535.4096168/94‑1 (MQ=60)

               AGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCG                                                                               >  SRR4302535.424416/1‑94 (MQ=60)

               AGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCG                                                                               >  SRR4302535.3888471/1‑94 (MQ=60)

                GTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGT                                                                              >  SRR4302535.2736807/1‑94 (MQ=60)

                 TCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTA                                                                             >  SRR4302535.1485091/1‑94 (MQ=60)

                  CGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTAC                                                                            >  SRR4302535.3170663/1‑94 (MQ=60)

                  CGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTAC                                                                            >  SRR4302535.2449788/1‑94 (MQ=60)

                   GCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACA                                                                           <  SRR4302535.497448/94‑1 (MQ=60)

                     CGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACC                                                                         >  SRR4302535.2967122/1‑94 (MQ=60)

                     CGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACC                                                                         >  SRR4302535.3277452/1‑94 (MQ=60)

                        AATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCC                                                                      <  SRR4302535.3113926/94‑1 (MQ=60)

                        AATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCC                                                                      >  SRR4302535.2250810/1‑94 (MQ=60)

                              GCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCG                                                                >  SRR4302535.4264909/1‑94 (MQ=60)

                               CCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGT                                                               >  SRR4302535.628652/1‑94 (MQ=60)

                               CCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGCGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGT                                                               >  SRR4302535.1034226/1‑94 (MQ=60)

                                CAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTC                                                              >  SRR4302535.4379161/1‑94 (MQ=60)

                                CAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTC                                                              <  SRR4302535.1661683/94‑1 (MQ=60)

                                 AAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCG                                                             <  SRR4302535.510369/94‑1 (MQ=60)

                                  AAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGC                                                            >  SRR4302535.2169575/1‑94 (MQ=60)

                                        AAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTT                                                      >  SRR4302535.1207718/1‑94 (MQ=60)

                                         AAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTC                                                     >  SRR4302535.3001886/1‑94 (MQ=60)

                                          AGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCA                                                    >  SRR4302535.1481296/1‑94 (MQ=60)

                                            GATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATT                                                  <  SRR4302535.4439055/94‑1 (MQ=60)

                                             ATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTA                                                 >  SRR4302535.2489240/1‑94 (MQ=60)

                                              TTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTAC                                                >  SRR4302535.4308097/1‑94 (MQ=60)

                                               TATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACC                                               <  SRR4302535.2658375/94‑1 (MQ=60)

                                                  CAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCAC                                            >  SRR4302535.1872384/1‑94 (MQ=60)

                                                     CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                         <  SRR4302535.215583/94‑1 (MQ=60)

                                                     CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                         <  SRR4302535.3752776/94‑1 (MQ=60)

                                                     CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                         <  SRR4302535.364703/94‑1 (MQ=60)

                                                     CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                         <  SRR4302535.2911035/94‑1 (MQ=60)

                                                     CGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAG                                         <  SRR4302535.2880166/94‑1 (MQ=60)

                                                      GATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGC                                        >  SRR4302535.2820093/1‑94 (MQ=60)

                                                      GATCGGCATAAAGAAGTCGGTGGCACTGATGACGCTGGCGGCATTGCCCAGATCGTCCACCGCCGCACCGTCGGGGGCTTCGTTGCCCACAAGG                                        >  SRR4302535.1413524/1‑94 (MQ=40)

                                                       ATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCA                                       >  SRR4302535.1823966/1‑94 (MQ=60)

                                                        TCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAA                                      >  SRR4302535.116764/1‑94 (MQ=60)

                                                          GGCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAAT                                    >  SRR4302535.1271377/1‑94 (MQ=60)

                                                           GCATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATT                                   >  SRR4302535.4517171/1‑94 (MQ=60)

                                                            CATAAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTC                                  <  SRR4302535.633485/94‑1 (MQ=60)

                                                               AAAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGA                               >  SRR4302535.1606652/1‑94 (MQ=60)

                                                                AAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAT                              >  SRR4302535.960251/1‑94 (MQ=60)

                                                                AAGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGAT                              >  SRR4302535.2232869/1‑94 (MQ=60)

                                                                 AGAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAGATTCGGATA                             >  SRR4302535.4416720/1‑94 (MQ=60)

                                                                  GAAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCA                            <  SRR4302535.376571/94‑1 (MQ=60)

                                                                   AAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAA                           >  SRR4302535.110629/1‑94 (MQ=60)

                                                                   AAGTCGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAA                           >  SRR4302535.2745360/1‑94 (MQ=60)

                                                                       CGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAA                       >  SRR4302535.1175909/1‑94 (MQ=60)

                                                                       CGGTGGTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAA                       <  SRR4302535.3085336/94‑1 (MQ=60)

                                                                          TGGTACTGATAGCGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTT                    <  SRR4302535.788786/94‑1 (MQ=60)

                                                                            GTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCG                  <  SRR4302535.3443454/94‑1 (MQ=60)

                                                                            GTACTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCG                  <  SRR4302535.2477090/94‑1 (MQ=60)

                                                                               CTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCT               >  SRR4302535.1298937/1‑94 (MQ=60)

                                                                               CTGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCT               <  SRR4302535.3485088/94‑1 (MQ=60)

                                                                                TGATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTG              <  SRR4302535.712029/94‑1 (MQ=60)

                                                                                  ATAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCT            <  SRR4302535.1565093/94‑1 (MQ=60)

                                                                                   AAACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTC           <  SRR4302535.1743855/94‑1 (MQ=60)

                                                                                    AACGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCA          >  SRR4302535.2753969/1‑94 (MQ=60)

                                                                                      CGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCATAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACT        <  SRR4302535.3781364/94‑1 (MQ=60)

                                                                                      CGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACT        <  SRR4302535.3781365/94‑1 (MQ=60)

                                                                                      CGCTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACT        <  SRR4302535.4571320/94‑1 (MQ=60)

                                                                                        CTGGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTAT      <  SRR4302535.1011177/94‑1 (MQ=60)

                                                                                        CTGGCGCCATTGCACAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTAT      <  SRR4302535.2696543/94‑1 (MQ=60)

                                                                                          GGCGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGC    <  SRR4302535.2565334/94‑1 (MQ=60)

                                                                                            CGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGCAG  <  SRR4302535.2495447/94‑1 (MQ=60)

                                                                                            CGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGCAG  <  SRR4302535.4542036/94‑1 (MQ=60)

ATCGCTGATGGCGTTAGTCGCCGCAATGCGGCCAAAATCGAAAGGATTATCAACGATCGGCATAAAGAAGTCGGTGGTACTGATAACGCTGGTGCCATTGCCCAGATCGTACACCGCCGCATCGTCGCGGGTTTCATTACCCACAAGCAAATTCGGATCAACAAACTTCGCCTGCTCACTATGCAG  >  NC_000913/1845760‑1845945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`