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	1,974,585	A→G	R193R (CGT→CGC)	motA ←	MotA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,974,585	0	A	G	99.1%	328.0 / NA	107	R193R (CGT→CGC)	motA	MotA
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (70/36); minor base T (0/1); total (70/37)
Fisher's exact test for biased strand distribution p-value = 3.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 116 total aligned reads displayed.

TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT  >  NC_000913/1974495‑1974674

tAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGAGCACCCAGCTCGGCGGCAGGGCg                                                                                         >  2:611297/1‑93 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCgg                                                                                        >  2:1662233/1‑92 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        >  1:4413238/1‑93 (MQ=255)

 aaTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGa                                                                                        <  1:1904753/93‑1 (MQ=255)

  aTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAt                                                                                       <  2:841962/93‑1 (MQ=255)

  aTGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAt                                                                                       <  1:2953550/93‑1 (MQ=255)

   tGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      >  1:4231556/1‑93 (MQ=255)

   tGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      <  2:4070015/93‑1 (MQ=255)

   tGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATc                                                                                      >  1:4575281/1‑93 (MQ=255)

     gggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCgg                                                                                    >  1:1011156/1‑93 (MQ=255)

     gggAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCgg                                                                                    >  1:2967929/1‑93 (MQ=255)

       gAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGTGCGATCGGCt                                                                                  >  1:1437589/1‑93 (MQ=255)

       gAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCt                                                                                  >  1:4169231/1‑93 (MQ=255)

         aataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGa                                                                                >  2:1039135/1‑93 (MQ=255)

         aataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGa                                                                                >  2:1394532/1‑93 (MQ=255)

         aataaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCACGGCGATCGGCTGa                                                                                >  2:1758558/1‑93 (MQ=255)

            aaatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAAcc                                                                             <  1:757548/93‑1 (MQ=255)

             aatCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCt                                                                            >  2:3877356/1‑93 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          <  2:2170105/93‑1 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          <  2:1906822/93‑1 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          >  2:3716606/1‑93 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          >  1:26734/1‑93 (MQ=255)

               tCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTaa                                                                          >  2:1652464/1‑93 (MQ=255)

                ccGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAc                                                                         <  1:3790824/93‑1 (MQ=255)

                ccGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAc                                                                         <  1:3779894/93‑1 (MQ=255)

                ccGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAc                                                                         <  1:2255679/93‑1 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgc                                                                       >  1:1501715/1‑93 (MQ=255)

                  gTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGAGATCGGCTGAACATAAcgc                                                                       >  2:359608/1‑93 (MQ=255)

                   tAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAAcgcg                                                                      >  2:3158500/1‑93 (MQ=255)

                    aaGCCAATAAAATGCCGAGGAAAGTCCCCGCCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCGGGGCGATCGGCTGAACCTAACGCGt                                                                     <  2:707494/93‑1 (MQ=255)

                    aaGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAGCGCGt                                                                     <  2:1182825/93‑1 (MQ=255)

                    aaGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGt                                                                     <  2:3607967/93‑1 (MQ=255)

                    aaGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGt                                                                     >  1:811091/1‑93 (MQ=255)

                      gCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGa                                                                   >  1:431059/1‑93 (MQ=255)

                       ccAATCAAATTTCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCAAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGaa                                                                  <  2:2946003/93‑1 (MQ=255)

                        cAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAAc                                                                 >  1:2541990/1‑93 (MQ=255)

                            aaaaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcc                                                             >  2:3958822/1‑93 (MQ=255)

                              aaTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAcccc                                                           <  1:837302/93‑1 (MQ=255)

                               aTGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAccccc                                                          >  1:246852/1‑93 (MQ=255)

                                tGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCa                                                         >  2:1216605/1‑93 (MQ=255)

                                tGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCa                                                         >  2:2481125/1‑93 (MQ=255)

                                 gCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCAt                                                        <  1:2259024/93‑1 (MQ=255)

                                 gCCGAGGAAAGTCCCAACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAANCTAACGCGTGAACGAccccnct                                                        >  1:4007434/1‑90 (MQ=255)

                                  ccGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCAtt                                                       <  1:1139349/93‑1 (MQ=255)

                                   cGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTa                                                      >  1:2872238/1‑93 (MQ=255)

                                    gAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTAc                                                     >  2:2791171/1‑93 (MQ=255)

                                    gAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTAc                                                     >  2:1937895/1‑93 (MQ=255)

                                    gAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTAc                                                     >  1:640363/1‑93 (MQ=255)

                                      ggAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGAGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAg                                                   >  2:1196715/1‑93 (MQ=255)

                                        aaaGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCGCCATTACaacg                                                 >  2:3263780/1‑90 (MQ=255)

                                        aaaGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGcc                                                 >  1:1479422/1‑93 (MQ=255)

                                           gTCACCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGca                                              >  2:3662958/1‑93 (MQ=255)

                                            tCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaa                                             >  2:1303714/1‑93 (MQ=255)

                                             ccccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaac                                            >  1:3232779/1‑93 (MQ=255)

                                              cccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaaca                                           <  1:1245796/93‑1 (MQ=255)

                                              cccACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaaca                                           >  1:3632876/1‑93 (MQ=255)

                                               ccaccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGcaacaa                                          >  2:4354522/1‑93 (MQ=255)

                                                caccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAAt                                         >  1:467751/1‑93 (MQ=255)

                                                caccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAAt                                         <  2:2157129/93‑1 (MQ=255)

                                                 cccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        <  1:2908769/92‑1 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        >  1:3120556/1‑93 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATa                                        >  1:2012892/1‑93 (MQ=255)

                                                 accaTCGCATGTGCGATAAGCGCACCCAGCTCGGAGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTGCAGCCGCAACAATa                                        >  1:694653/1‑93 (MQ=255)

                                                  ccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAc                                       >  2:4486341/1‑93 (MQ=255)

                                                  ccaTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAc                                       >  1:3651465/1‑93 (MQ=255)

                                                    aTCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAACCCCATTACAGCCGCAACAATACCa                                     >  1:1819767/1‑93 (MQ=255)

                                                     tCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaa                                    <  1:1641724/93‑1 (MQ=255)

                                                     tCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCaa                                    >  1:2059856/1‑93 (MQ=255)

                                                         aTGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGc                                >  1:1873776/1‑93 (MQ=255)

                                                          tgtgCGATAATCGCACCCATCTCGGCGGCAGGTCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGcc                               <  1:805414/93‑1 (MQ=255)

                                                          tgtgCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGcc                               >  2:2959461/1‑93 (MQ=255)

                                                           gtgCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCg                              >  2:1051848/1‑93 (MQ=255)

                                                              cGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGaa                           <  1:1634751/93‑1 (MQ=255)

                                                               gATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAg                          <  1:1500952/93‑1 (MQ=255)

                                                               gATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAg                          >  2:4175508/1‑93 (MQ=255)

                                                               gATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAg                          <  1:3881695/93‑1 (MQ=255)

                                                               gATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAg                          >  2:4106103/1‑93 (MQ=255)

                                                                aTAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGt                         <  2:1491211/93‑1 (MQ=255)

                                                                aTAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGt                         >  2:64007/1‑93 (MQ=255)

                                                                 tAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTg                        >  1:2401003/1‑93 (MQ=255)

                                                                 tAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTg                        >  1:359003/1‑93 (MQ=255)

                                                                  aaGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGa                       <  1:2771029/93‑1 (MQ=255)

                                                                  aaGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGa                       <  1:436238/93‑1 (MQ=255)

                                                                   aGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGGGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAg                      >  1:3040310/1‑93 (MQ=255)

                                                                    gcgcACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGt                     >  1:196156/1‑93 (MQ=255)

                                                                       cACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTccc                  <  2:1952816/93‑1 (MQ=255)

                                                                       cACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTccc                  >  1:2871149/1‑93 (MQ=255)

                                                                        aCCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTcccc                 <  2:2979431/93‑1 (MQ=255)

                                                                         cccAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCg                >  2:396049/1‑93 (MQ=255)

                                                                           cAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGAc              >  1:1673282/1‑93 (MQ=255)

                                                                            aGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGAcc             >  2:3413356/1‑93 (MQ=255)

                                                                             gCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCa            >  2:2483909/1‑93 (MQ=255)

                                                                                cggcggCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGCAGTGAGTCCCCGACCAgcg         >  1:4394761/1‑93 (MQ=255)

                                                                                cggcggCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAgcg         >  1:1675580/1‑93 (MQ=255)

                                                                                  gcggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGcc       >  1:1885815/1‑93 (MQ=255)

                                                                                    ggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAg     <  1:4129728/93‑1 (MQ=255)

                                                                                    ggcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAg     >  2:1118864/1‑93 (MQ=255)

                                                                                     gcAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGa    >  2:1940968/1‑93 (MQ=255)

                                                                                      cAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGAc   <  1:4069692/93‑1 (MQ=255)

                                                                                       aGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACt  >  1:1677977/1‑93 (MQ=255)

TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT  >  NC_000913/1974495‑1974674

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTT  >  NC_000913/1974493‑1974677

GCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGC                                                                                             <  SRR4302535.3791292/94‑1 (MQ=60)

 CTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCG                                                                                            <  SRR4302535.876702/94‑1 (MQ=60)

 CTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCG                                                                                            <  SRR4302535.2655497/94‑1 (MQ=60)

  TAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGA                                                                                           >  SRR4302535.4443443/1‑94 (MQ=60)

   AATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGAT                                                                                          <  SRR4302535.1918463/94‑1 (MQ=60)

    ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                         >  SRR4302535.4606461/1‑94 (MQ=60)

    ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                         >  SRR4302535.4260516/1‑94 (MQ=60)

    ATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATC                                                                                         <  SRR4302535.2974299/94‑1 (MQ=60)

      GGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGG                                                                                       >  SRR4302535.2988757/1‑94 (MQ=60)

      GGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGG                                                                                       >  SRR4302535.1018339/1‑94 (MQ=60)

        GGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGTGCGATCGGCT                                                                                     >  SRR4302535.1447863/1‑94 (MQ=60)

        GGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCT                                                                                     >  SRR4302535.4197782/1‑94 (MQ=60)

              AAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCT                                                                               <  SRR4302535.762877/94‑1 (MQ=60)

                ATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAA                                                                             >  SRR4302535.26942/1‑94 (MQ=60)

                  CCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACG                                                                           <  SRR4302535.2271738/94‑1 (MQ=60)

                  CCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACG                                                                           <  SRR4302535.3816963/94‑1 (MQ=60)

                  CCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACG                                                                           <  SRR4302535.3805982/94‑1 (MQ=60)

                   CGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGC                                                                          >  SRR4302535.1512518/1‑94 (MQ=60)

                     TAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGT                                                                        >  SRR4302535.816761/1‑94 (MQ=60)

                       AGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGA                                                                      >  SRR4302535.434060/1‑94 (MQ=60)

                         CCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAAC                                                                    <  SRR4302535.3812445/94‑1 (MQ=60)

                         CCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAAC                                                                    >  SRR4302535.2560297/1‑94 (MQ=60)

                            ATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAC                                                                 >  SRR4302535.2222899/1‑94 (MQ=60)

                              AAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCC                                                               <  SRR4302535.2754342/94‑1 (MQ=60)

                                AATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCC                                                             <  SRR4302535.843178/94‑1 (MQ=60)

                                AATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCC                                                             >  SRR4302535.248544/1‑94 (MQ=60)

                                  TGCCGAGGAAAGTCCCAACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAANCTAACGCGTGAACGACCCCNCT                                                           >  SRR4302535.4034852/1‑94 (MQ=60)

                                   GCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATT                                                          <  SRR4302535.2275107/94‑1 (MQ=60)

                                    CCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTA                                                         >  SRR4302535.2892592/1‑94 (MQ=60)

                                    CCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTA                                                         <  SRR4302535.1147469/94‑1 (MQ=60)

                                     CGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTAC                                                        >  SRR4302535.644838/1‑94 (MQ=60)

                                      GAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACA                                                       <  SRR4302535.3129675/94‑1 (MQ=60)

                                         GAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCC                                                    >  SRR4302535.1490007/1‑94 (MQ=60)

                                              TCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAAC                                               >  SRR4302535.3255196/1‑94 (MQ=60)

                                               CCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACA                                              >  SRR4302535.4661081/1‑94 (MQ=60)

                                               CCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACA                                              >  SRR4302535.3658053/1‑94 (MQ=60)

                                                CCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAA                                             <  SRR4302535.1254685/94‑1 (MQ=60)

                                                 CCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAAT                                            >  SRR4302535.471023/1‑94 (MQ=60)

                                                  CACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATA                                           >  SRR4302535.2027392/1‑94 (MQ=60)

                                                  CACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATA                                           >  SRR4302535.3142286/1‑94 (MQ=60)

                                                  CACCATCGCATGTGCGATAAGCGCACCCAGCTCGGAGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTGCAGCCGCAACAATA                                           >  SRR4302535.699527/1‑94 (MQ=60)

                                                   CCCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAC                                          <  SRR4302535.2929326/94‑1 (MQ=60)

                                                   ACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATAC                                          >  SRR4302535.3676748/1‑94 (MQ=60)

                                                     CATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCA                                        <  SRR4302535.1845228/94‑1 (MQ=60)

                                                     CATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGAACCCCATTACAGCCGCAACAATACCA                                        >  SRR4302535.1832914/1‑94 (MQ=60)

                                                      ATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAA                                       >  SRR4302535.2074697/1‑94 (MQ=60)

                                                       TCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAA                                      <  SRR4302535.1653593/94‑1 (MQ=60)

                                                          CATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGC                                   >  SRR4302535.1887278/1‑94 (MQ=60)

                                                            TGTGCGATAATCGCACCCATCTCGGCGGCAGGTCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCG                                 <  SRR4302535.811065/94‑1 (MQ=60)

                                                                CGATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAG                             <  SRR4302535.1646563/94‑1 (MQ=60)

                                                                CGATAAGCGCACCCAGCTCGGCGGCAGGGAGATCGGCTGAACCTAACGCGTGAACGACCCGCATTACAGCCGCAACAATACCAAACGCCGGAAG                             >  SRR4302535.597156/1‑94 (MQ=60)

                                                                 GATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGT                            <  SRR4302535.3908331/94‑1 (MQ=60)

                                                                 GATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGT                            <  SRR4302535.1511750/94‑1 (MQ=60)

                                                                  ATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTG                           >  SRR4302535.361490/1‑94 (MQ=60)

                                                                  ATAAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTG                           >  SRR4302535.2418272/1‑94 (MQ=60)

                                                                    AAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAG                         <  SRR4302535.439279/94‑1 (MQ=60)

                                                                    AAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAG                         <  SRR4302535.2790761/94‑1 (MQ=60)

                                                                    AAGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGGGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAG                         >  SRR4302535.3061605/1‑94 (MQ=60)

                                                                     AGCGCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGT                        >  SRR4302535.197505/1‑94 (MQ=60)

                                                                        GCACCCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCC                     >  SRR4302535.2891491/1‑94 (MQ=60)

                                                                            CCAGCTCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGAC                 >  SRR4302535.1685393/1‑94 (MQ=60)

                                                                                 TCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGCAGTGAGTCCCCGACCAGCG            >  SRR4302535.4424836/1‑94 (MQ=60)

                                                                                 TCGGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCG            >  SRR4302535.1687713/1‑94 (MQ=60)

                                                                                   GGCGGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCC          >  SRR4302535.1899401/1‑94 (MQ=60)

                                                                                      GGCAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGA       <  SRR4302535.4157987/94‑1 (MQ=60)

                                                                                        CAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT     <  SRR4302535.4097543/94‑1 (MQ=60)

                                                                                        CAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT     >  SRR4302535.1634107/1‑94 (MQ=60)

                                                                                        CAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACT     >  SRR4302535.1690127/1‑94 (MQ=60)

                                                                                        CAGGGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGAACAGCGCCAGACT     >  SRR4302535.4206342/1‑94 (MQ=60)

                                                                                           GGCGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTT  <  SRR4302535.675526/94‑1 (MQ=60)

GCTAATGGGGAAATAAATCCGTAAGCCAATAAAATGCCGAGGAAAGTCCCCACCATCGCATGTGCGATAAGCGCACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTT  >  NC_000913/1974493‑1974677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 2 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`